NeuroTOC

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AbstractOptical amplification, crucial for modern communication, primarily relies on erbium-doped fibre amplifiers (EDFAs)1,2. Yet, EDFAs only cover a portion of the low-loss spectrum of optical fibres. This has motivated the development of amplifiers operating beyond the erbium gain window. Pioneering work on optical parametric amplifiers (OPAs)3,4using intrinsic third-order optical nonlinearity has led to demonstrations of increased channel capacity. OPAs offer high gain, can reach the 3-dB quantum limit for phase-preserving amplifiers and exhibit unidirectional operation. However, power requirements for highly nonlinear fibres3,5–8or bulk waveguides9,10have impeded their adoption. By contrast, OPAs based on integrated photonic circuits offer the advantages of substantially increased mode confinement and optical nonlinearity but have been limited in bandwidth11,12. We overcome this challenge by using low-loss gallium phosphide-on-silicon dioxide13–15photonic integrated circuits (PICs) and attain up to 35 dB of parametric gain with waveguides only a few centimetres long in a compact footprint of 0.25 square millimetres. Fibre-to-fibre net gain exceeding 10 dB across an ultra-broad bandwidth of approximately 140 nm (that is, 17 THz) is achieved, with a threefold increase in the gain window compared with C-band EDFAs. We further demonstrate a high dynamic range for input signals, spanning six orders of magnitude, while maintaining a low noise figure. We exploit these performance characteristics to amplify coherent communication signals. This marks, to our knowledge, the first ultra-broadband, high-gain, continuous-wave amplification in a photonic chip, opening up new capabilities for next-generation integrated photonics.

AbstractAntigenic variation is an immune evasion strategy used by many different pathogens. It involves the periodic, non-random switch in the expression of different antigens throughout an infection. How the observed hierarchy in antigen expression is achieved has remained a mystery1,2. A key challenge in uncovering this process has been the inability to track transcriptome changes and potential genomic rearrangements in individual cells during a switch event. Here we report the establishment of a highly sensitive single-cell RNA sequencing approach for the model protozoan parasiteTrypanosoma brucei. This approach has revealed genomic rearrangements that occur in individual cells during a switch event. Our data show that following a double-strand break in the transcribed antigen-coding gene—an important trigger for antigen switching—the type of repair mechanism and the resultant antigen expression depend on the availability of a homologous repair template in the genome. When such a template was available, repair proceeded through segmental gene conversion, creating new, mosaic antigen-coding genes. Conversely, in the absence of a suitable template, a telomere-adjacent antigen-coding gene from a different part of the genome was activated by break-induced replication. Our results show the critical role of repair sequence availability in the antigen selection mechanism. Furthermore, our study demonstrates the power of highly sensitive single-cell RNA sequencing methods in detecting genomic rearrangements that drive transcriptional changes at the single-cell level.

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AbstractHepatic stellate cells (HSCs) have a central pathogenetic role in the development of liver fibrosis. However, their fibrosis-independent and homeostatic functions remain poorly understood1–5. Here we demonstrate that genetic depletion of HSCs changes WNT activity and zonation of hepatocytes, leading to marked alterations in liver regeneration, cytochrome P450 metabolism and injury. We identify R-spondin 3 (RSPO3), an HSC-enriched modulator of WNT signalling, as responsible for these hepatocyte-regulatory effects of HSCs. HSC-selective deletion ofRspo3phenocopies the effects of HSC depletion on hepatocyte gene expression, zonation, liver size, regeneration and cytochrome P450-mediated detoxification, and exacerbates alcohol-associated and metabolic dysfunction-associated steatotic liver disease.RSPO3expression decreases with HSC activation and is inversely associated with outcomes in patients with alcohol-associated and metabolic dysfunction-associated steatotic liver disease. These protective and hepatocyte-regulating functions of HSCs via RSPO3 resemble the R-spondin-expressing stromal niche in other organs and should be integrated into current therapeutic concepts.

AbstractIn a subset of children and adolescents, SARS-CoV-2 infection induces a severe acute hyperinflammatory shock1termed multisystem inflammatory syndrome in children (MIS-C) at four to eight weeks after infection. MIS-C is characterized by a specific T cell expansion2and systemic hyperinflammation3. The pathogenesis of MIS-C remains largely unknown. Here we show that acute MIS-C is characterized by impaired reactivation of virus-reactive memory T cells, which depends on increased serum levels of the cytokine TGFβ resembling those that occur during severe COVID-19 (refs.4,5). This functional impairment in T cell reactivity is accompanied by the presence of TGFβ-response signatures in T cells, B cells and monocytes along with reduced antigen-presentation capabilities of monocytes, and can be reversed by blocking TGFβ. Furthermore, T cell receptor repertoires of patients with MIS-C exhibit expansion of T cells expressing TCRVβ21.3, resembling Epstein–Barr virus (EBV)-reactive T cell clones capable of eliminating EBV-infected B cells. Additionally, serum TGFβ in patients with MIS-C can trigger EBV reactivation, which is reversible with TGFβ blockade. Clinically, the TGFβ-induced defect in T cell reactivity correlates with a higher EBV seroprevalence in patients with MIS-C compared with age-matched controls, along with the occurrence of EBV reactivation. Our findings establish a connection between SARS-CoV-2 infection and COVID-19 sequelae in children, in which impaired T cell cytotoxicity triggered by TGFβ overproduction leads to EBV reactivation and subsequent hyperinflammation.

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AbstractNanoribbons, nanometre-wide strips of a two-dimensional material, are a unique system in condensed matter. They combine the exotic electronic structures of low-dimensional materials with an enhanced number of exposed edges, where phenomena including ultralong spin coherence times1,2, quantum confinement3and topologically protected states4,5can emerge. An exciting prospect for this material concept is the potential for both a tunable semiconducting electronic structure and magnetism along the nanoribbon edge, a key property for spin-based electronics such as (low-energy) non-volatile transistors6. Here we report the magnetic and semiconducting properties of phosphorene nanoribbons (PNRs). We demonstrate that at room temperature, films of PNRs show macroscopic magnetic properties arising from their edge, with internal fields of roughly 240 to 850 mT. In solution, a giant magnetic anisotropy enables the alignment of PNRs at sub-1-T fields. By leveraging this alignment effect, we discover that on photoexcitation, energy is rapidly funnelled to a state that is localized to the magnetic edge and coupled to a symmetry-forbidden edge phonon mode. Our results establish PNRs as a fascinating system for studying the interplay between magnetism and semiconducting ground states at room temperature and provide a stepping-stone towards using low-dimensional nanomaterials in quantum electronics.

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Highlights from theSciencefamily of journals

Pelage coloration, which serves numerous functions, is crucial to the evolution of behavior, physiology, and habitat preferences of mammals. However, little is known about the coloration of Mesozoic mammaliaforms that coevolved with dinosaurs. In this study, we used a dataset of melanosome (melanin-containing organelle) morphology and quantitatively measured hair colors from 116 extant mammals to reliably reconstruct the coloration of six Mesozoic mammaliaforms, including a previously undescribed euharamiyidan. Unlike the highly diverse melanosomes discovered in feathered dinosaurs, hairs in six mammaliaforms of different lineages and diverse ecomorphotypes showed uniform melanosome geometry, corresponding to dark-brown coloration consistent with crypsis and nocturnality. Our results suggest that the melanosome variation and color expansion seen in extant mammals may have occurred during their rapid radiation and diversification after the Cretaceous-Paleogene extinction.

Nitrous oxide (N2O) is a potent greenhouse gas and the main stratospheric ozone-depleting agent, yet its sources are not well resolved. In this work, we experimentally show a N2O production pathway not previously considered in greenhouse gas budgets, which we name photochemodenitrification. Sunlight induces substantial and consistent N2O production under oxic abiotic conditions in fresh and marine waters. We measured photochemical N2O production rates using isotope tracers and determined that nitrite is the main substrate and that nitrate can also contribute after being photoreduced to nitrite. Additionally, this N2O production was strongly correlated to the radiation dose. Photochemodenitrification exceeded biological N2O production in surface waters. Although previously overlooked, this process may contribute considerably to global N2O emissions through its occurrence in fresh and marine surface waters.

The flagellum ofTrypanosoma bruceidrives the parasite’s characteristic screw-like motion and is essential for its replication, transmission, and pathogenesis. However, the molecular details of this process remain unclear. Here, we present high-resolution (up to 2.8 angstrom) cryo–electron microscopy structures ofT. bruceiflagellar doublet microtubules (DMTs). Integrated modeling identified 154 different axonemal proteins inside and outside the DMT and, together with genetic and proteomic interrogation, revealed conserved and trypanosome-specific foundations of flagellum assembly and motility. We captured axonemal dynein motors in their pre–power stroke state. Comparing atomic models between pre– and post–power strokes defined how dynein structural changes drive sliding of adjacent DMTs during flagellar beating. This study illuminates structural dynamics underlying flagellar motility and identifies pathogen-specific proteins to consider for therapeutic interventions targeting neglected diseases.

Current organic light-emitting diode (OLED) technology uses light-emitting molecules in a molecular host. We report green circularly polarized luminescence (CPL) in a chirally ordered supramolecular assembly, with 24% dissymmetry in a triazatruxene (TAT) system. We found that TAT assembled into helices with a pitch of six molecules, associating angular momentum to the valence and conduction bands and obtaining the observed CPL. Cosublimation of TAT as the “guest” in a structurally mismatched “host” enabled fabrication of thin films in which chiral crystallization was achieved in situ by thermally triggered nanophase segregation of dopant and host while preserving film integrity. The OLEDs showed external quantum efficiencies of up to 16% and electroluminescence dissymmetries ≥10%. Vacuum deposition of chiral superstructures opens new opportunities to explore chiral-driven optical and transport phenomena.

Antarctic ice shelves buttress the grounded ice sheet, mitigating global sea level rise. However, fundamental mechanical properties, such as the ice flow law and viscosity structure, remain under debate. In this work, by leveraging remote-sensing data and physics-informed deep learning, we provide evidence over several ice shelves that the flow law follows a grain size–sensitive composite rheology in the compression zone. In the extension zone, we found that ice exhibits anisotropic properties. We constructed ice shelf–wide anisotropic viscosity maps that capture the suture zones, which inhibit rift propagation. The inferred stress exponent near the grounding zone dictates the grounding-line ice flux and grounding line stability, whereas the inferred viscosity maps inform the prediction of rifts. Both are essential for predicting the future mass loss of the Antarctic Ice Sheet.

Interstellar dust grains cause extinction (absorption and scattering) of light from background astronomical sources. The spectral shape of the extinction curve depends on the dust composition. We used low-resolution optical spectra to measure the extinction curve of 130 million stars. By inverting these data, we mapped the extinction curve parameterR(V) within the Milky Way in three dimensions and within the Magellanic Clouds in two dimensions. These maps provide improved extinction corrections for astronomical observations. We find thatR(V) varies with extinction, consistent with dust grains growing by accretion in low-extinction regions and by coagulation in higher-extinction regions. Star-forming regions have highR(V) values, indicating either preferential destruction of small dust grains or additional supply of large dust grains in those regions.

Rattan palms illuminate the drivers of biodiversity in tropical Asia

Membrane projections from muscle cells enable signaling in the developing mouse heart

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Expedition finds the virus in 13 bird and seal species around the Antarctic Peninsula

Implications draw on the history of transformative information systems from the past

Floods threaten to spread sediments laden with toxicants

In trio of studies, scientists explore life in the mysterious hadal zone

The use of water as a weapon in highly industrialized areas in the Russo-Ukrainian war has resulted in catastrophic economic and environmental damages. We analyze environmental effects caused by the military destruction of the Kakhovka Dam. We link field, remote sensing, and modeling data to demarcate the disaster’s spatial-temporal scales and outline trends in reestablishment of damaged ecosystems. Although media attention has focused on the immediate impacts of flooding on society, politics, and the economy, our results show that toxic contamination within newly exposed sediments of the former reservoir bed poses a largely overlooked long-term threat to freshwater, estuarine, and marine ecosystems. The continued use of water as a weapon may lead to even greater risks for people and the environment.

A partnership can be demanding, and as with any couple, can have good days and bad. The United States–Canada relationship is most definitely having a bad one. It’s difficult to fully comprehend all the dimensions of the current threats to one of the world’s strongest, longest, and multifaceted alliances. From contemptuous musings on annexation to a tariff war that could wreak economic havoc on both sides of the border, the insults and aggravations are stoking uncertainty about a relationship that has flourished for decades. This includes a strongly intertwined connection between Canadian and American science—one that must continue in these challenging times.

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Distributed across two continents and thousands of islands, the Asian tropics are among the most species-rich areas on Earth. The origins of this diversity, however, remain poorly understood. Here, we reveal and classify contributions of individual tropical Asian regions to their overall diversity by leveraging species-level phylogenomic data and new fossils from the most species-rich Asian palm lineage, the rattans and relatives (Arecaceae, Calamoideae). Radiators (Borneo) generate and distribute diversity, incubators (Indochina, New Guinea, and Sulawesi) produce diversity in isolation, corridors (Java, Maluku, Sumatra, and the Thai-Malay Peninsula) connect neighboring regions, and accumulators (Australia, India, Palawan, and the Philippines) acquire diversity generated elsewhere. These contrasting contributions can be explained by differences in region size and isolation, elucidating how the unique island-dominated geography of the Asian tropics drives their outstanding biodiversity.

Although the global economy requires geological resource mining, production has substantial environmental impacts, including the use of regional available water. In this study, we shed light on the global production capacity of 32 mined geological resources, considering regional water availability as a constraint. We found that current resource mining greatly exceeds regional water constraints for several, notably copper (37% of current production exceeds available water capacity) in 2010. Changing the location of production to regions of lower water stress would alleviate current exceedances of water constraints; however, considering economic factors shows that this is not always feasible. Future demand for geological resources is expected to require a considerable increase in water consumption. Considering the constraints of water resources in geological resource production is crucial for sustainability.

At least 1.1 million years old, a fossil face suggests more than one type of early human inhabited Europe

RFK Jr. has claimed conflicts of interest must be rooted out of key CDC panel

Cochlear implants give deaf kids unprecedented access to sound. But insisting they avoid using sign language may be risky

Editors’ selections from the current scientific literature

The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet microtubules (DMTs). In this work, we present cryo–electron microscopy structures of DMTs from two trypanosomatid species,Leishmania tarentolaeandCrithidia fasciculata, at resolutions up to 2.7 angstrom. The structures revealed 27 trypanosomatid-specific microtubule inner proteins, a specialized dynein-docking complex, and the presence of paralogous proteins that enable higher-order periodicities or proximal-distal patterning. Leveraging the genetic tractability of trypanosomatid species, we quantified the location and contribution of each structure-identified protein to swimming behavior. Our study shows that proper B-tubule closure is critical for flagellar motility, exemplifying how integrating structural identification with systematic gene deletion can dissect individual protein contributions to flagellar motility.

Fetal and infant brains offer clues to when human experience begins

Piezoelectricity is primarily observed in noncentrosymmetric insulators or wide bandgap semiconductors. We report the observation of the piezoelectric (PE) effect in half-Heusler (HH) narrow-bandgap semiconductors TiNiSn, ZrNiSn, and TiCoSb. These materials exhibit shear PE strain coefficients that reach ~38 and 33 picocoulombs per newton in ZrNiSn and TiCoSb, respectively, which are high values for noncentrosymmetric nonpolar materials. We demonstrated a TiCoSb-based PE sensor with a large voltage response and capable of charging a capacitor. The PE effect in HHs remains thermally stable up to 1173 kelvin, underscoring their potential for high-temperature applications. Our observations suggest that these HH narrow-bandgap semiconductors may find promising applications for advanced multifunctional technologies.

A deep-learning model infers large-scale dynamics of Antarctic ice shelves

The ozonolytic deconstruction of aromatics remains a challenge in organic chemistry. Ozone preferentially reacts with alkenes over arenes, meaning that once the initial aromatic cleavage occurs, the dearomatized products are inherently more reactive than the starting materials. Consequently, the process cannot be halted, resulting in full oxidation. Addressing this challenge requires subverting intrinsic rules of chemoselectivity to transform a less reactive substrate in the presence of a more reactive one. We demonstrate that this concept can be achieved by using photoexcited nitroarenes. Crucial to the success of this chemoselective process is the use of a nitroarene that is preferentially excitable to a triplet π,π* state over the n,π* state. This switch in excited-state configuration provides an otherwise inaccessible manifold, in which oxidative cleavage is diverted toward aromatics in the presence of alkenes.

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AbstractThe Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes and biomarkers) and to use the HRA to characterize changes that occur with aging, disease and other perturbations. HRA v.2.0 covers 4,499 unique anatomical structures, 1,195 cell types and 2,089 biomarkers (such as genes, proteins and lipids) from 33 ASCT+B tables and 65 3D Reference Objects linked to ontologies. New experimental data can be mapped into the HRA using (1) cell type annotation tools (for example, Azimuth), (2) validated antibody panels or (3) by registering tissue data spatially. This paper describes HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interfaces, flexible hybrid cloud infrastructure and previews atlas usage applications.

AbstractThe availability of single-cell transcriptomics has allowed the construction of reference cell atlases, but their usefulness depends on the quality of dataset integration and the ability to map new samples. Previous benchmarks have compared integration methods and suggest that feature selection improves performance but have not explored how best to select features. Here, we benchmark feature selection methods for single-cell RNA sequencing integration using metrics beyond batch correction and preservation of biological variation to assess query mapping, label transfer and the detection of unseen populations. We reinforce common practice by showing that highly variable feature selection is effective for producing high-quality integrations and provide further guidance on the effect of the number of features selected, batch-aware feature selection, lineage-specific feature selection and integration and the interaction between feature selection and integration models. These results are informative for analysts working on large-scale tissue atlases, using atlases or integrating their own data to tackle specific biological questions.

AbstractThe human genome contains instructions to transcribe more than 200,000 RNAs. However, many RNA transcripts are generated from the same gene, resulting in alternative isoforms that are highly similar and that remain difficult to quantify. To evaluate the ability to study RNA transcript expression, we profiled seven human cell lines with five different RNA-sequencing protocols, including short-read cDNA, Nanopore long-read direct RNA, amplification-free direct cDNA and PCR-amplified cDNA sequencing, and PacBio IsoSeq, with multiple spike-in controls, and additional transcriptome-wideN6-methyladenosine profiling data. We describe differences in read length, coverage, throughput and transcript expression, reporting that long-read RNA sequencing more robustly identifies major isoforms. We illustrate the value of the SG-NEx data to identify alternative isoforms, novel transcripts, fusion transcripts andN6-methyladenosine RNA modifications. Together, the SG-NEx data provide a comprehensive resource enabling the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.

AbstractThe Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.

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AbstractRNA velocity exploits the temporal information contained in spliced and unspliced RNA counts to infer transcriptional dynamics. Existing velocity models often rely on coarse biophysical simplifications or numerical approximations to solve the underlying ordinary differential equations (ODEs), which can compromise accuracy in challenging settings, such as complex or weak transcription rate changes across cellular trajectories. Here we present cell2fate, a formulation of RNA velocity based on a linearization of the velocity ODE, which allows solving a biophysically more accurate model in a fully Bayesian fashion. As a result, cell2fate decomposes the RNA velocity solutions into modules, providing a biophysical connection between RNA velocity and statistical dimensionality reduction. We comprehensively benchmark cell2fate in real-world settings, demonstrating enhanced interpretability and power to reconstruct complex dynamics and weak dynamical signals in rare and mature cell types. Finally, we apply cell2fate to the developing human brain, where we spatially map RNA velocity modules onto the tissue architecture, connecting the spatial organization of tissues with temporal dynamics of transcription.

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AbstractCellular organelles undergo constant morphological changes and dynamic interactions that are fundamental to cell homeostasis, stress responses and disease progression. Despite their importance, quantifying organelle morphology and motility remains challenging due to their complex architectures, rapid movements and the technical limitations of existing analysis tools. Here we introduce Nellie, an automated and unbiased pipeline for segmentation, tracking and feature extraction of diverse intracellular structures. Nellie adapts to image metadata and employs hierarchical segmentation to resolve sub-organellar regions, while its radius-adaptive pattern matching enables precise motion tracking. Through a user-friendly Napari-based interface, Nellie enables comprehensive organelle analysis without coding expertise. We demonstrate Nellie’s versatility by unmixing multiple organelles from single-channel data, quantifying mitochondrial responses to ionomycin via graph autoencoders and characterizing endoplasmic reticulum networks across cell types and time points. This tool addresses a critical need in cell biology by providing accessible, automated analysis of organelle dynamics.

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AbstractThe dynamics of neuron populations commonly evolve on low-dimensional manifolds. Thus, we need methods that learn the dynamical processes over neural manifolds to infer interpretable and consistent latent representations. We introduce a representation learning method, MARBLE, which decomposes on-manifold dynamics into local flow fields and maps them into a common latent space using unsupervised geometric deep learning. In simulated nonlinear dynamical systems, recurrent neural networks and experimental single-neuron recordings from primates and rodents, we discover emergent low-dimensional latent representations that parametrize high-dimensional neural dynamics during gain modulation, decision-making and changes in the internal state. These representations are consistent across neural networks and animals, enabling the robust comparison of cognitive computations. Extensive benchmarking demonstrates state-of-the-art within- and across-animal decoding accuracy of MARBLE compared to current representation learning approaches, with minimal user input. Our results suggest that a manifold structure provides a powerful inductive bias to develop decoding algorithms and assimilate data across experiments.

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AbstractAccurate segmentation of objects in microscopy images remains a bottleneck for many researchers despite the number of tools developed for this purpose. Here, we present Segment Anything for Microscopy (μSAM), a tool for segmentation and tracking in multidimensional microscopy data. It is based on Segment Anything, a vision foundation model for image segmentation. We extend it by fine-tuning generalist models for light and electron microscopy that clearly improve segmentation quality for a wide range of imaging conditions. We also implement interactive and automatic segmentation in a napari plugin that can speed up diverse segmentation tasks and provides a unified solution for microscopy annotation across different microscopy modalities. Our work constitutes the application of vision foundation models in microscopy, laying the groundwork for solving image analysis tasks in this domain with a small set of powerful deep learning models.

AbstractGeneralist methods for cellular segmentation have good out-of-the-box performance on a variety of image types; however, existing methods struggle for images that are degraded by noise, blurring or undersampling, all of which are common in microscopy. We focused the development of Cellpose3 on addressing these cases and here we demonstrate substantial out-of-the-box gains in segmentation and image quality for noisy, blurry and undersampled images. Unlike previous approaches that train models to restore pixel values, we trained Cellpose3 to output images that are well segmented by a generalist segmentation model, while maintaining perceptual similarity to the target images. Furthermore, we trained the restoration models on a large, varied collection of datasets, thus ensuring good generalization to user images. We provide these tools as ‘one-click’ buttons inside the graphical interface of Cellpose as well as in the Cellpose API.

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AbstractAdvances in computational structure prediction will vastly augment the hundreds of thousands of currently available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive. Foldseek-Multimer computes complex alignments from compatible chain-to-chain alignments, identified by efficiently clustering their superposition vectors. Foldseek-Multimer is 3–4 orders of magnitudes faster than the gold standard, while producing comparable alignments; this allows it to compare billions of complex pairs in 11 h. Foldseek-Multimer is open-source software available at GitHub viahttps://github.com/steineggerlab/foldseek/,https://search.foldseek.com/search/and the BFMD database.

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AbstractEndothelial cells (ECs) help maintain the blood–brain barrier but deteriorate in many neurodegenerative disorders. Here we show, using a specialized method to isolate EC and microglial nuclei from postmortem human cortex (92 donors, 50 male and 42 female, aged 20–98 years), that intranuclear cellular indexing of transcriptomes and epitopes enables simultaneous profiling of nuclear proteins and RNA transcripts at a single-nucleus resolution. We identify a disease-associated subset of capillary ECs in Alzheimer’s disease, amyotrophic lateral sclerosis and frontotemporal degeneration. These capillaries exhibit reduced nuclear β-catenin and β-catenin-downstream genes, along with elevated TNF/NF-κB markers. Notably, these transcriptional changes correlate with the loss of nuclear TDP-43, an RNA-binding protein also depleted in neuronal nuclei. TDP-43 disruption in human and mouse ECs replicates these alterations, suggesting that TDP-43 deficiency in ECs is an important factor contributing to blood–brain barrier breakdown in neurodegenerative diseases.

AbstractDepolarization of axons is necessary for somatic action potentials to trigger axonal neurotransmitter release. Here we show that striatal cholinergic interneurons (ChIs) and nicotinic receptors (nAChRs) on mouse dopamine axons interrupt this relationship. After nAChR-mediated depolarization, dopamine release by subsequent depolarization events was suppressed for ~100 ms. This suppression was not due to depletion of dopamine or acetylcholine, but to a limited reactivation of dopamine axons after nAChR-mediated depolarization, and is more prominent in dorsal than in ventral striatum. In vivo, nAChRs predominantly depressed dopamine release, as nAChR antagonism in dorsal striatum elevated dopamine detected with optic-fiber photometry of dopamine sensor GRABDA2mand promoted conditioned place preference. Our findings reveal that ChIs acting via nAChRs transiently limit the reactivation of dopamine axons for subsequent action potentials in dopamine neurons and therefore generate a dynamic inverse scaling of dopamine release according to ChI activity.

AbstractRecent studies suggest the existence of brain-first and body-first subtypes within the Lewy body disorder (LBD) spectrum, including Parkinson’s disease. These studies primarily focused on α-synuclein propagation through the parasympathetic vagal and olfactory bulb routes, leaving the possibility of a sympathetic nervous system spreading route unexplored. In the present study, we analyzed two postmortem datasets, which included 173 and 129 cases positive for Lewy pathology. We observed a clear distinction between brain-first and body-first subtypes in early prediagnostic cases with mild Lewy pathology. Brain-first cases displayed minimal peripheral organ pathology in prediagnostic phases, contrasting with marked autonomic involvement in prediagnostic body-first cases. Utilizing the SuStaIn machine learning algorithm, we identified two distinct body-first subtypes, one with vagal predominance and another with sympathetic predominance, in equal proportions. Our study supports the existence of three prediagnostic LBD subtypes and highlights the sympathetic nervous system alongside the parasympathetic system in LBD onset and progression.

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AbstractThe hippocampus is critical for memory, imagination and constructive reasoning. Recent models have suggested that its neuronal responses can be well explained by state spaces that model the transitions between experiences. Here we use simulations and hippocampal recordings to reconcile these views. We show that if state spaces are constructed compositionally from existing building blocks, or primitives, hippocampal responses can be interpreted as compositional memories, binding these primitives together. Critically, this enables agents to behave optimally in new environments with no new learning, inferring behavior directly from the composition. We predict a role for hippocampal replay in building and consolidating these compositional memories. We test these predictions in two datasets by showing that replay events from newly discovered landmarks induce and strengthen new remote firing fields. When the landmark is moved, replay builds a new firing field at the same vector to the new location. Together, these findings provide a framework for reasoning about compositional memories and demonstrate that such memories are formed in hippocampal replay.

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AbstractHere we report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in aDrosophilamodel ofC9orf72repeat expansion, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD), and in human postmortem ALS spinal cord. We performed lipidomics on C9 ALS/FTDDrosophila, induced pluripotent stem (iPS) cell neurons and postmortem FTD brain tissue. This revealed a common and specific reduction in phospholipid species containing polyunsaturated fatty acids (PUFAs). Feeding C9 ALS/FTD flies PUFAs yielded a modest increase in survival. However, increasing PUFA levels specifically in neurons of C9 ALS/FTD flies, by overexpressing fatty acid desaturase enzymes, led to a substantial extension of lifespan. Neuronal overexpression of fatty acid desaturases also suppressed stressor-induced neuronal death in iPS cell neurons of patients with both C9 and TDP-43 ALS/FTD. These data implicate neuronal fatty acid saturation in the pathogenesis of ALS/FTD and suggest that interventions to increase neuronal PUFA levels may be beneficial.

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AbstractHigher cortical areas carry a wide range of sensory, cognitive and motor signals mixed in heterogeneous responses of single neurons tuned to multiple task variables. Dimensionality reduction methods that rely on correlations between neural activity and task variables leave unknown how heterogeneous responses arise from connectivity to drive behavior. We develop the latent circuit model, a dimensionality reduction approach in which task variables interact via low-dimensional recurrent connectivity to produce behavioral output. We apply the latent circuit inference to recurrent neural networks trained to perform a context-dependent decision-making task and find a suppression mechanism in which contextual representations inhibit irrelevant sensory responses. We validate this mechanism by confirming the behavioral effects of patterned connectivity perturbations predicted by the latent circuit model. We find similar suppression of irrelevant sensory responses in the prefrontal cortex of monkeys performing the same task. We show that incorporating causal interactions among task variables is critical for identifying behaviorally relevant computations from neural response data.

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AbstractWe offer a novel motivational account of romantic love, which portrays it as a means to the end of feeling significant and worthy. According to the model, falling in love with a partner depends on the actor's perceptions that (1) the partner possesses meritorious characteristics, and (2) that they appreciate the actor and view them as significant. We assume that these two factors multiplicatively combine with the magnitude of actor's quest for significance to determine the likelihood of actor becoming enamored with partner. The multiplicative model has two major implications: 1. If any one of the partner'smerit,appreciation, or actor'ssignificance questfactors falls below its respective threshold of acceptability (such that it is subjectively non-existent), the likelihood of falling in love will be negligible. 2. Above their acceptability thresholds, levels of (partner's)merit,appreciationand (actor's)significance questfactors compensate for one another. A partner's lower standing on merit or appreciation is compensated in its impact on falling in love by the partner's higher standing on the remaining dimension. Furthermore, lower levels of either or both of these factors are compensated for by the actor's higher level of significance quest.Our model affords a broad account of diverse love phenomena, allows the derivation of several specific hypotheses supported by prior close-relations research as well as new data, and it offers novel avenues for further research on classic issues in romantic love. The discussion considers our model's unique implications and examines its relation to other theories of love.

AbstractMany motivational constructs are opaque “black boxes,” and should be replaced by an explicit account of the underlying psychological mechanisms. The theory of motivational systems has begun to provide such an account. I recently contributed to this tradition with a general architecture of motivation, which connects “energization” and “direction” through the goal-setting activity of emotions, and serves as an evolutionary grounded map of motivational processes.

AbstractWhole Trait Theory (and other dynamic theories of personality) can illuminate the process by which motivational states become traits. Mental computational processes constitute part of the explanatory mechanisms that drive trait manifestations. Empirical work on Whole Trait Theory may inform future research directions on mental computational processes.

AbstractSome constructs in motivation science are certainly underdeveloped and some motivation researchers may work with underspecified constructs, as suggested by Murayama and Jach (M&J). However, this is not indicative of a general problem in motivation science. Many motivation theories focus on specific mechanisms underlying motivated behavior and thus have already adopted the computational process perspective that M&J call for.

AbstractMurayama and Jach argue that it is not clearly specified how motivation constructs produce behavior and that this black box should be unpacked. We argue that the authors overlook important classic theory and highlight recent research programs that already started unboxing. We feel that without relying on the mechanisms that such programs uncover, the proposed computational approach will be fruitless.

AbstractShared intentionality is the derived hominin motivation and skills to align mental states. Research on the role of interdependence in the phylogeny of shared intentionality has only considered the archeological record ofHomo heidelbergensis. But ethnographic and fossil data must be considered, too. Doing so suggests that shared intentionality may have been favored inHomo erectusto support persistence hunting.

AbstractInnovations, such as symbolic artifacts, are a product of cognitive abilities but also of cultural context. Factors that may determine the emergence and retention of an innovation include the population's pre-existing cultural repertoire, exposure to relevant ways of thinking, and the invention's utility. Thus, we suggest that the production of symbolic artifacts is not guaranteed even in cognitively advanced societies.

AbstractUsing modern hunter-gatherers to infer about earlyHomo sapiensonly works if at least (a) modern hunter-gatherers represent an unbiased sample of humanity, and (b) modern hunter-gatherers act in ways similar to the behavior of earlyHomo sapiens. Both of these are false, leading to the problem of whether we can draw conclusions about earlyHomo sapiensfrom modern hunter-gatherers.

AbstractWe comment on the consequences of the target article for language evolution research. We propose that the default assumption should be that of language-readiness in extinct hominins, and the integration of different types of available evidence from multiple disciplines should be used to assess the likely extent of the realization of this readiness. The role of archaeological evidence should be reconsidered.

AbstractStibbard-Hawkes' taphonomic findings are valuable, and his call for caution warranted, but the hazards he raises are being mitigated by a multi-pronged approach; current research on behavioural/cognitive modernity is not based solely on material chronology. Theories synthesize data from archaeology, anthropology, psychology, neuroscience, and genetics, and predictions arising from these theories are tested with mathematical and agent-based models.

AbstractThere are indeed questionable motivation constructs in psychology. The diagnosis and proposed remedies in the target article both neglect the crucial consideration that all tendencies to behaviour compete for the same finite set of degrees of freedom. Action selection also has irreducibly economic aspects which should constrain motivation constructs and already inform healthy research programmes.

AbstractThough we see the potential for benefits from the development of process-oriented approaches, we argue that it falls prey to many of the same critiques raised about the existing construct level of analysis. The construct-level approach will likely dominate motivation research until we develop computational models that are not only accurate, but also broadly usable.

AbstractI argue that Murayama and Jach's claim that higher-order motivational constructs face the “black-box” problem is misconceived because it doesn't clearly distinguish between personal and subpersonal explanations. To solve it they propose interpreting motivations as causal effects of mental computational processes. I suggest that their solution might be more compellingly presented as providing a fictionalist perspective on some personal-level constructs.

AbstractMurayama and Jach raise a key problem in behavioral sciences, to which we suggest evolutionary science can provide a solution. We emphasize the role of adaptive mechanisms in shaping behavior and argue for the integration of hierarchical theories of goal-directed cognition and behavioral flexibility, in order to unravel the motivations behind actions that, in themselves, seem disconnected from adaptive goals.

AbstractThe article provides an important warning but its general conclusions should be nuanced: (i) When there is no evidence for it, we should depart from the hypothesis that a species lacks a particular cognitive capacity, and (ii) inferences from absence of evidence can be epistemically sound and scientifically strategic in cognitive and linguistic archaeology.

AbstractThe absence of symbolic material cultural objects in the archaeological record does not prove absence of symbolic cognition. Sometimes perishable materials are selected for symbolic roles, for practical concerns or to indicate a temporary condition. Also some symbolic functions may predate the use of durable materials. Finally, child play and artisan experimentations usually involve cheap and perishable materials. These are symbolic and representational activities that do not leave a material trace.

AbstractStibbard-Hawkes challenges the link between symbolic material evidence and behavioural modernity. Extending this to non-human species, we find that personal adornment, decoration, figurative art, and musical instruments may not uniquely distinguish human cognition. These common criteria may ineffectively distinguish symbolic from non-symbolic cognition or symbolic cognition is not uniquely human. It highlights the need for broader comparative perspectives.

AbstractWe welcome Stibbard-Hawkes's empirical contributions and discussion of interpretive challenges for archaeology, but question some of his characterizations and conclusions. Moving beyond critique, it is time to develop new research methods that eschew simplistic modern/premodern binaries. We advocate an inductive, probabilistic approach using multiple lines of evidence to infer the causes and consequences of behavioral variability across time and space.

AbstractOur species' behavioral and cognitive evolution constitute a key research topic across many scientific disciplines. Based on ethnographic hunter-gatherer data, Stibbard-Hawkes challenges the common link made between past material culture and cognitive capacities. Despite this adequate criticism, archaeology must retain a central role for studying these issues due to its unique access to relevant empirical evidence in deep time.

AbstractI expand Stibbard-Hawkes' exploration of symbolism and cognition to suggest that we also ought to reconsider the strength of connections between cognition and technological complexity. Using early weaponry as a case study I suggest that complexity may be “hidden” in early tools, and further highlight that assessments of technologies as linear and progressive have roots in Western colonial thought.

AbstractStibbard-Hawkes presents a much-needed case for distinguishing between different types of evidence for cognition in past cultures. However, he does not outline an applicable approach for moving forward in making claims about the cognition of past cultures. We present an initial model for calibrating both absolute and comparative claims about past cultures' cognition and other traits.

AbstractThe target article explores material culture datasets from three African forager groups. After demonstrating that these modern, contemporary human populations would leave scant evidence of symbolic behaviour or material complexity, it cautioned against using material culture as a barometer for human cognition in the deep past. Twenty-one commentaries broadly support or expand these conclusions. A minority offer targeted demurrals, highlighting (1) the soundness of reasoning from absence; and questioning (2) the “cognitively modern” null; (3) the role of hunter-gatherer ethnography; and (4) the pertinence of the inferential issues identified in the target article. In synthesising these discussions, this reply addresses all four points of demurral in turn, and concludes that there is much to be gained from shifting our null assumptions and reconsidering the probabilistic inferential links between past material culture and cognition.

AbstractMurayama and Jach claim that current motivational constructs do not specify causal processes (black-box problem) and thatmental computational processessolve this problem. We argue, process-focused research requires theoretical frameworks addressing situational variations, individual differences, and their interaction. Classic achievement motivation theory provides comprehensive models with empirically measurable process-related constructs and predictions. Recent developments build on this, addressing motivation, action, and their socio-cultural and lifespan context. Theory-freemental computational processescannot do any of that.

AbstractMurayama and Jach rightfully aim to conceptualize motivation as an emergent property of a dynamic system of interacting elements. However, they do not embrace the ontological and paradigmatic constraints of the dynamic systems approach. They therefore miss the very process of emergence and how it can be formally modeled and tested by specific types of computer simulation.

AbstractMurayama and Jach point out that we do not sufficiently understand the constructs and mental computations underlying higher-order motivated behaviors. Although this may be generally true, we would like to add and contribute to the discussion by outlining how interdisciplinary research onnovelty-evoked explorationhas advanced the study of learning and curiosity.

AbstractEndogenous reward (intrinsic reward at will) is afiat currencythat isoccasionedby steps toward any goals which are challenging and/or uncommon enough to prevent its debasement by inflation. A “theory of mental computational processes” should propose what properties let goals grow from appetites for endogenous rewards. Endogenous reward may be the universal selective factor in all modifiable mental processes.

AbstractThe proposed “black-box” problem and its solution are drawn from the same substance-oriented framework. This framework's assumptions have consequences that re-create the black-box problem at a foundational level. Specifically, Murayama and Jach's solution fails to explain novel behavior that emerges through an organism's development. A process-oriented theoretical shift provides an ontological explanation for emergent behavior and eliminates the black-box problem altogether.

AbstractWe argue that the target article's computational/reductionistic approach to motivation is insufficient to explain the energization of human behavior, because such explanation requires broad consideration of “what people are trying to do.” We illustrate what is gained by retaining (rather than jettisoning) higher-order motivation constructs and show that the authors’ approach assumes, but fails to name, such constructs.

AbstractAlthough higher-level constructs often fail to explain the mechanisms underlying motivation, we argue that purely mechanistic approaches have limitations. Lower-level neural data help us identify “biologically plausible” mechanisms, while higher-level constructs are critical to formulate measurable behavioral outcomes when constructing computational models. Therefore, we propose that a multi-level, multi-measure approach is required to fully unpack the black box of motivated behavior.

AbstractMurayama and Jach criticize the use of high-level motivational constructs in psychology, urging psychologists to “unpack” the black box. These constructs are alleged to be “psychological constructions” with no causal powers of their own. I argue that this view is mistaken, and that high-level motivational constructs are causal even when unpacked in terms of underlying computational, algorithmic, and implementational processes.

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AbstractCells secrete a large variety of extracellular vesicles (EVs) to engage in cell-to-cell and cell-to-environment intercellular communication. EVs are functionally involved in many physiological and pathological processes by interacting with cells that facilitate transfer of proteins, lipids and genetic information. However, our knowledge of EVs is incomplete. Here we show that cells actively release exceptionally large (up to 20 µm) membrane-enclosed vesicles that exhibit active blebbing behavior, and we, therefore, have termed them blebbisomes. Blebbisomes contain an array of cellular organelles that include functional mitochondria and multivesicular endosomes, yet lack a definable nucleus. We show that blebbisomes can both secrete and internalize exosomes and microvesicles. Blebbisomes are released from normal and cancer cells, can be observed by direct imaging of cancer cells in vivo and are present in normal bone marrow. We demonstrate that cancer-derived blebbisomes contain a plethora of inhibitory immune checkpoint proteins, including PD-L1, PD-L2, B7-H3, VISTA, PVR and HLA-E. These data identify a very large, organelle-containing functional EV that act as cell-autonomous mobile communication centres capable of integrating and responding to signals in the extracellular environment.

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AbstractTissue patterning coordinates morphogenesis, cell dynamics and fate specification. Understanding how precision in patterning is robustly achieved despite inherent developmental variability during mammalian embryogenesis remains a challenge. Here, based on cell dynamics quantification and simulation, we show how salt-and-pepper epiblast and primitive endoderm (PrE) cells pattern the inner cell mass of mouse blastocysts. Coupling cell fate and dynamics, PrE cells form apical polarity-dependent actin protrusions required for RAC1-dependent migration towards the surface of the fluid cavity, where PrE cells are trapped due to decreased tension. Concomitantly, PrE cells deposit an extracellular matrix gradient, presumably breaking the tissue-level symmetry and collectively guiding their own migration. Tissue size perturbations of mouse embryos and their comparison with monkey and human blastocysts further demonstrate that the fixed proportion of PrE/epiblast cells is optimal with respect to embryo size and tissue geometry and, despite variability, ensures patterning robustness during early mammalian development.

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AbstractDuring early embryogenesis, fast mitotic cycles without interphase lead to a decrease in cell size, while scaling mechanisms must keep cellular structures proportional to cell size. For instance, as cells become smaller, if the position of nuclear envelope reformation (NER) did not adapt, NER would have to occur beyond the cell boundary. Here we found that NER position in anaphase scales with cell size via changes in chromosome motility, mediated by cytoplasmic flows that themselves scale with cell size. Flows are a consequence of friction between viscous cytoplasm and bulky cargo transported by dynein on astral microtubules. As an emerging property, confinement in cells of different sizes yields scaling of cytoplasmic flows. Thus, flows behave like a cell geometry sensor: astral microtubules approach the boundary causing flow velocity changes, which then affect the velocity of chromosome separation, thus scaling NER.

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AbstractThe dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.

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AbstractTemporal prediction is a fundamental function of neural systems. Recent results show that humans anticipate future events by calculating probability density functions, rather than hazard rates. However, direct neural evidence for this hypothesized mechanism is lacking. We recorded neural activity using magnetoencephalography as participants anticipated auditory and visual events distributed in time. We show that temporal anticipation, measured as reaction times, approximates the event probability density function, but not hazard rate. Temporal anticipation manifests as spatiotemporally patterned activity in three anatomically and functionally distinct parieto-temporal and sensorimotor cortical areas. Each of these areas revealed a marked neural signature of anticipation: Prior to sensory cues, activity in a specific frequency range of neural oscillations, spanning alpha and beta ranges, encodes the event probability density function. These neural signals predicted reaction times to imminent sensory cues. These results demonstrate that supra-modal representations of probability density across cortex underlie the anticipation of future events.

AbstractAlthough complexes with monatomic zero-valent main group centers have been reported, diatomic zero-valent complexes are extremely rare and all previously reported examples were stabilized by either carbene or silylene ligands. Here, we present the isolation of diatomic E(0)-E(0) (E = Sn, Pb) species supported by two [N{CH₂CH₂NPiPr₂}₃Sn] fragments. The reaction of trilithium salt N{CH2CH2NLiPiPr2}3with SnCl2yields complex [N{CH2CH2NPiPr2}3]2Sn3(1) with a Sn3chain. The reduction of the mixture of1and SnCl2with KC8produces the catenated Sn4chain [N{CH2CH2NPiPr2}3Sn2]2(2), featuring a diatomic Sn(0)-Sn(0) unit. Further reduction of2with KC8yields the alkali metal ion-bridged complex [N{CH2CH2NPiPr2}3SnK]2(3). Moreover, the reaction of3with PbI2and KC8affords [N{CH2CH2NPiPr2}3SnPb]2(4), which can also be generated by the reaction of KC8with PbI2and [N{CH2CH2NPiPr2}3SnLi]2(5). Complex4features a diatomic Pb(0)-Pb(0) unit, representing a heavy diatomic zero-valent main group complex. The presence of diatomic E(0)-E(0) (E = Sn, Pb) units in complexes2and4, respectively, is further confirmed by computational studies.

AbstractCodanin-1 (CDAN1) is an essential and ubiquitous protein named after congenital dyserythropoietic anemia type I, an autosomal recessive disease that manifests from mutations inCDAN1orCDIN1(CDAN1interactingnuclease 1). CDAN1 interacts with CDIN1 and the paralogous histone H3-H4 chaperones ASF1A (Anti-SilencingFunction 1 A) and ASF1B. However, CDAN1 function remains unclear. Here, we analyze CDAN1 complexes using biochemistry, single-particle cryo-EM, and structural predictions. We find that CDAN1 dimerizes and assembles into cytosolic complexes with CDIN1 and multiple copies of ASF1A/B. One CDAN1 can engage two ASF1 through two B-domains commonly found in ASF1 binding partners and two helices that mimic histone H3 binding. We additionally show that ASF1A and ASF1B have different requirements for CDAN1 engagement. Our findings explain how CDAN1 sequesters ASF1A/B by occupying all functional binding sites known to facilitate histone chaperoning and provide molecular-level insights into this enigmatic complex.

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AbstractOverall artificial photosynthesis, as a promising approach for sunlight-driven CO2recycling, requires photocatalysts with efficient light adsorption and separate active sites for coupling with H2O oxidation. Here we show a In-based metal–organic framework (MOF) heterostructure, i.e., In-porphyrin (In-TCPP) nanosheets enveloping an In-NH2-MIL-68 (M68N) core, via a facile one-pot synthesis that utilises competitive nucleation and growth of two organic linkers with In nodes. The coherent interfaces of the core@shell MOFs assure the structural stability of heterostructure, which will function as heterojunctions to facilitate the efficient transfer of photogenerated charge for overall photosynthesis. The In-TCPP shell in MOFs heterostructure improves CO2adsorption capabilities and visible light absorption to enhance the photocatalytic CO2reduction. Simultaneously, In-O sites in M68N core efficiently catalyze H2O oxidation, achieving high yields of HCOOH (397.5 μmol g−1h−1) and H2O2(321.2 μmol g−1h−1) under focused sunlight irradiation. The superior performance of this heterostructure in overall photosynthesis, coupled with its straightforward synthesis, shows great potential for mitigating carbon emissions and producing valuable chemicals using solar energy.

AbstractLactate dehydrogenase B (LDHB) fuels oxidative cancer cell metabolism by converting lactate to pyruvate. This study uncovers LDHB’s role in countering mitochondria-associated ferroptosis independently of lactate’s function as a carbon source. LDHB silencing alters mitochondrial morphology, causes lipid peroxidation, and reduces cancer cell viability, which is potentiated by the ferroptosis inducer RSL3. Unlike LDHA, LDHB acts in parallel with glutathione peroxidase 4 (GPX4) and dihydroorotate dehydrogenase (DHODH) to suppress mitochondria-associated ferroptosis by decreasing the ubiquinone (coenzyme Q, CoQ) to ubiquinol (CoQH2) ratio. Indeed, supplementation with mitoCoQH2 (mitochondria-targeted analogue of CoQH2) suppresses mitochondrial lipid peroxidation and cell death after combined LDHB silencing and RSL3 treatment, consistent with the presence of LDHB in the cell fraction containing the mitochondrial inner membrane. Addressing the underlying molecular mechanism, an in vitro NADH consumption assay with purified human LDHB reveals that LDHB catalyzes the transfer of reducing equivalents from NADH to CoQ and that the efficiency of this reaction increases by the addition of lactate. Finally, radiation therapy induces mitochondrial lipid peroxidation and reduces tumor growth, which is further enhanced when combined with LDHB silencing. Thus, LDHB-mediated lactate oxidation drives the CoQ-dependent suppression of mitochondria-associated ferroptosis, a promising target for combination therapies.

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AbstractGene expression (GE) and alternative splicing (AS) contribute to the formation of new interaction networks with potentially significant cellular functions. Here, we investigate ageing in theDrosophilafemale germline stem cell (GSC) niche and describe functional changes in both GE and AS. The GSC niche comprises three types of support cells, whose ageing transcriptomes reveal differential GE and AS variations related to cell adhesion, cytoskeleton and neural signalling. Because each population show distinctive GE and AS changes, niche cell types possess unique ageing signatures. Depending on the cell population, groups of genes display changes in both GE and AS, revealing a coordinated regulation of transcription and splicing during niche ageing. One such gene isFasciclin 2, a neural adhesion molecule that we find is essential for niche functioning. Furthermore, genes involved in AS undergo changes in GE and/or AS themselves, providing a mechanistic explanation for the coordination of these two processes during niche ageing. This is the case of the splicing factor Smu1, described here as a key element necessary for ovarian niche homeostasis.

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AbstractRecently light-driven microdrones have been demonstrated, making use of plasmonic nanomotors based on directional resonant chiral light scattering. These nanomotors can be addressed individually, without requiring the tracking of a focused laser, leading to exceptional 2D maneuverability which renders microdrones a versatile robotic platform in aqueous environments. Here, we incorporate a light-operated manipulator, a plasmonic nano-tweezer, into the microdrone platform, rendering it a microrobot by enabling precise, all-optical transport and delivery of single nanoparticles suspended in solution. The plasmonic nano-tweezer consists of a resonant cross-antenna nanostructure exhibiting a central near-field hot spot, extending the ability of traditional optical tweezers based on focused laser beams to the trapping of nanoparticles. However, most of plasmonic nano-tweezers are fixed to the substrates and lack mobility. Our plasmonic microrobot utilizes circularly polarized light to control both motors and for stable trapping of a 70-nanometer fluorescent nanodiamond in the cross-antenna center. Complex sequences of microrobot operations, including trap-transport-release-trap-transport actions, demonstrate the microrobot’s versatility and precision in picking up and releasing nanoparticles. Our microrobot design opens potential avenues in advancing nanotechnology and life sciences, with applications in targeted drug delivery, single-cell manipulation, and by providing an advanced quantum sensing platform, facilitating interdisciplinary research at the nanoscale.

AbstractFetal cell ablation models are crucial for studying congenital diseases, organ regeneration, and xenotransplantation. However, conventional knockout models offer limited control over disease severity, while conditional ablation models often require fetus-harming inducers. In the present study, we demonstrate that the inducible caspase 9 system enables precise targeting of fetal nephron progenitor cells in mice through the intrinsic apoptotic pathway. Using a safe, placenta-permeable inducer, this system facilitates specific, rapid, and efficient cell ablation. The system’s temporal control allows precise adjustment of disease severity, generating reproducible models ranging from congenital kidney deficiency to severe chronic kidney disease. Cells with low expression levels of inducible caspase 9 and those in solid organs are less susceptible to apoptosis. However, this limitation can be overcome by inhibiting the X-linked inhibitor of apoptosis protein, thereby expanding the system’s applicability. Additionally, this model provides a developmental environment suitable for chimeric kidney regeneration. This system advances understanding of induced cell death mechanisms, enhances pathological research tools, and supports therapeutic development in kidney disease and xenotransplantation applications.

AbstractIn photosynthetic organisms, light acts as an environmental signal to control their development and physiology, as well as energy source to drive the conversion of CO2into carbohydrates used for growth or storage. The main storage carbohydrate in green algae is starch, which accumulates during the day and is broken down at night to meet cellular energy demands. The signaling role of light quality in the regulation of starch accumulation remains unexplored. Here, we identify PHOTOTROPIN-MEDIATED SIGNALING KINASE 1 (PMSK1) as a key regulator of starch metabolism inChlamydomonas reinhardtii. In its phosphorylated form (PMSK1-P), it activates GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAP1), promoting starch biosynthesis. We show that blue light, perceived by PHOTOTROPIN, induces PMSK1 dephosphorylation that in turn represses GAP1 mRNA levels and reduces starch accumulation. These findings reveal a previously uncharacterized blue light-mediated signaling pathway that advances our understanding of photoreceptor-controlled carbon metabolism in microalgae.

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AbstractLocalization of mRNAs to neuronal terminals, coupled to local translation, has emerged as a prevalent mechanism controlling the synaptic proteome. However, the physiological regulation and function of this process in the context of mature in vivo memory circuits has remained unclear. Here, we combined synaptosome RNA profiling with whole brain high-resolution imaging to uncover mRNAs with different localization patterns in the axons ofDrosophilaMushroom Body memory neurons, some exhibiting regionalized, input-dependent, recruitment along axons. By integrating transcriptome-wide binding approaches and functional assays, we show that the conserved Imp RNA binding protein controls the transport of mRNAs to Mushroom Body axons and characterize a mutant in which this transport is selectively impaired. Using this unique mutant, we demonstrate that axonal mRNA localization is required for long-term, but not short-term, behavioral memory. This work uncovers circuit-dependent mRNA targeting in vivo and demonstrates the importance of local RNA regulation in memory consolidation.

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AbstractHeterogeneous single-atom systems demonstrate potential to break performance limitations of single-atom catalysts through synergy interactions. The synergy in heterogeneous single atoms strongly dependes on their anchoring sites. Herein, we reveal the site-specific synergy in heterogeneous single atoms for oxygen evolution. The RuTIrV/CoOOH is fabricated by anchoring Ru single atoms onto three-fold facial center cubic hollow sites and Ir single atoms onto oxygen vacancy sites on CoOOH. Moreover, IrTRuV/CoOOH is also prepared by switching the anchoring sites of single atoms. Electrochemical measurements demonstrate the RuTIrV/CoOOH exhibits enhanced OER performance compared to IrTRuV/CoOOH. In-situ spectroscopic and mechanistic studies indicate that Ru single atoms at three-fold facial center cubic hollow sites serve as adsorption sites for key reaction intermediates, while Ir single atoms at oxygen vacancy sites stabilize the *OOH intermediates via hydrogen bonding interactions. This work discloses the correlation between the synergy in heterogeneous single atoms and their anchoring sites.

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AbstractThe goals of the current study were to determine the efficacy in major depressive disorder (MDD) of a shortened, computer-augmented cognitive behavioral therapy (CCBT) protocol and to determine brain plasticity effects following CCBT. Seventy-two MDD participants were randomized to CCBT or waitlist control groups and compared to 40 healthy controls (HCs). Functional MRI data were collected for all participants and repeated for patients following CCBT (five therapist-administered manualized CBT sessions plus computer training exercises). Linear mixed-effects models evaluated changes in depression scores throughout treatment and in connectivity from pre- to post-CCBT. Linear regression models compared connectivity differences between groups (MDD vs. HC). Following CCBT, there were decreases in MADRS and BDI (ps < 0.001); there was more negative connectivity of dlPFC with sgACC and DMN with sgACC (ps < 0.002); and there was more positive connectivity of FPN with nucleus accumbens, bilateral amygdalae, bilateral hippocampi, and sgACC and of DMN with ventral and dorsal bilateral anterior insulae (ps < 0.01). There were no associations between change in MADRS and change in connectivity; however, there was an association between change in BDI and change in FPN–sgACC connectivity (p= 0.01). A shortened CBT schedule coupled with home computer exercises was associated with decreased depression symptoms and augmented PFC connectivity with multiple subcortical regions. One possible mechanism of the CCBT intervention is modulating PFC connectivity with subcortical regions, influencing top-down control of affective processes dysregulated in MDD.

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AbstractMolecular neuroimaging techniques, like PET and SPECT, offer invaluable insights into the brain’s in-vivo biology and its dysfunction in neuropsychiatric patients. However, the transition of molecular neuroimaging into diagnostics and precision medicine has been limited to a few clinical applications, hindered by issues like practical feasibility, high costs, and high between-subject heterogeneity of neuroimaging measures. In this study, we explore the use of normative modelling (NM) to identify individual patient alterations by describing the physiological variability of molecular functions. NM potentially addresses challenges such as small sample sizes and diverse acquisition protocols typical of molecular neuroimaging studies. We applied NM to two PET radiotracers targeting the dopaminergic system ([11C]-(+)-PHNO and [18F]FDOPA) to create a reference-cohort model of healthy controls. The models were subsequently utilized on different independent cohorts of patients with psychosis in different disease stages and treatment outcomes. Our results showed that patients with psychosis exhibited a higher degree of extreme deviations (~3-fold increase) than controls, although this pattern was heterogeneous, with minimal overlap of extreme deviations topology (max 20%). We also confirmed that striatal [18F]FDOPA signal, when referenced to a normative distribution, can predict treatment response (striatal AUC ROC: 0.77–0.83). In conclusion, our results indicate that normative modelling can be effectively applied to molecular neuroimaging after proper harmonization, enabling insights into disease mechanisms and advancing precision medicine. In addition, the method is valuable in understanding the heterogeneity of patient populations and can contribute to maximising cost efficiency in studies aimed at comparing cases and controls.

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AbstractThe increased prevalence of opioid use disorder (OUD) makes it imperative to disentangle the biological mechanisms contributing to individual differences in OUD vulnerability. OUD shows strong heritability, however genetic variants contributing to vulnerability remain poorly defined. We performed a genome-wide association study using over 850 male and female heterogeneous stock (HS) rats to identify genes underlying behaviors associated with OUD such as nociception, as well as heroin-taking, extinction and seeking behaviors. By using an animal model of OUD, we were able to identify genetic variants associated with distinct OUD behaviors while maintaining a uniform environment, an experimental design not easily achieved in humans. Furthermore, we used a novel non-linear network-based clustering approach to characterize rats based on OUD vulnerability to assess genetic variants associated with OUD susceptibility. Our findings confirm the heritability of several OUD-like behaviors, including OUD susceptibility. Additionally, several genetic variants associated with nociceptive threshold prior to heroin experience, heroin consumption, escalation of intake, and motivation to obtain heroin were identified.Tom1, a microglial component, was implicated for nociception. Several genes involved in dopaminergic signaling, neuroplasticity and substance use disorders, includingBrwd1,Pcp4, Phb1l2andMmp15were implicated for the heroin traits. Additionally, an OUD vulnerable phenotype was associated with genetic variants for consumption and break point, suggesting a specific genetic contribution for OUD-like traits contributing to vulnerability. Together, these findings identify novel genetic markers related to the susceptibility to OUD-relevant behaviors in HS rats.

AbstractRising adolescent suicide rates present a growing unmet need. Childhood trauma (CT) has been associated with altered cortisol dynamics and immune cell glucocorticoid reactivity, yet their additive longer-term contributions to later suicide outcomes are less clear. The current study compared CT scores, resting salivary free cortisol and mononuclear cell gene expression levels of the nuclear receptor, subfamily 3, member 1 (NR3C1) coding the glucocorticoid receptor, and its co-chaperons FKBP prolyl isomerase 5 (FKBP5) and KIT Ligand (KITLG), between a cohort of adolescents presenting with a suicidal crisis requiring hospital treatment, and matched healthy controls. Childhood trauma scores and glucocorticoid measures were significantly altered among suicidal adolescents, and CT scores correlated with mononuclear cell glucocorticoid transcripts. Both CT scores and glucocorticoid measures explained substantial additive portions of the variance in adolescent suicidality. Long-term perturbations in cortisol dynamics and immune cell glucocorticoid response elements denote dysregulated immune stress reactivity, and may possess value in prediction and point to modifiable-risk factors in prevention of clinically significant suicidality during the brittle period of adolescence, years after childhood trauma exposure.

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AbstractGenetic variants linked to autism are thought to change cognition and behaviour by altering the structure and function of the brain. Although a substantial body of literature has identified structural brain differences in autism, it is unknown whether autism-associated common genetic variants are linked to changes in cortical macro- and micro-structure. We investigated this using neuroimaging and genetic data from adults (UK Biobank, N = 31,748) and children (ABCD, N = 4928). Using polygenic scores and genetic correlations we observe a robust negative association between common variants for autism and a magnetic resonance imaging derived phenotype for neurite density (intracellular volume fraction) in the general population. This result is consistent across both children and adults, in both the cortex and in white matter tracts, and confirmed using polygenic scores and genetic correlations. There were no sex differences in this association. Mendelian randomisation analyses provide no evidence for a causal relationship between autism and intracellular volume fraction, although this should be revisited using better powered instruments. Overall, this study provides evidence for shared common variant genetics between autism and cortical neurite density.

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AbstractPrediction from polygenic scores may be confounded by sources of passive gene-environment correlation (rGE; e.g. population stratification, assortative mating, and environmentally mediated effects of parental genotype on child phenotype). Using genomic data from 10 000 twin pairs, we asked whether polygenic scores from the most recent externalising genome-wide association study predict conduct problems, ADHD symptomology and callous-unemotional traits, and whether these predictions are biased by rGE. We ran regression models including within-family and between-family polygenic scores, to separate the direct genetic influence on a trait from environmental influences that correlate with genes (indirect genetic effects). Findings suggested that this externalising polygenic score is a good index of direct genetic influence on conduct and ADHD-related symptoms across development, with minimal bias from rGE, although the polygenic score predicted less variance in CU traits. Post-hoc analyses showed some indirect genetic effects acting on a common factor indexing stability of conduct problems across time and contexts.

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AbstractNon-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer’s disease, and Parkinson’s disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.

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AbstractRecently published large-scale randomised controlled trials (RCTs) have questioned the efficacy of preventive interventions in individuals at clinical high risk for psychosis (CHR-P). We conducted a systematic review and meta-analysis to include this new evidence and provide future directions for the field. We followed the PRISMA guidelines and a pre-registered protocol, with a literature search conducted from inception to November 2023. We included RCTs that collected data on psychosis transition (the primary outcome) in CHR-P. Secondary outcomes were symptoms severity and functioning. Investigated time points were 6,12,24,36, and +36 months. We used odd ratios (ORs) and standardised mean differences (SMD) as summary outcomes. Heterogeneity was estimated with the Higgins I2. Twenty-four RCTs, involving 3236 CHR-P individuals, were included. Active interventions were Cognitive Behavioural Therapy (CBT), family-focused therapy, Integrated Psychological Therapy, antipsychotics, omega-3 fatty acids, CBT plus risperidone, minocycline, and other non-pharmacological approaches (cognitive remediation, sleep-targeted therapy, brain stimulation). Results showed no evidence that any of the investigated active interventions had a sustained and robust effect on any of the investigated outcomes in CHR-P, when compared to control interventions, including CBT on transition to psychosis at 12 months (9 RCTs; OR: 0.64; 95% CI: 0.39–1.06; I2: 21%;P= 0.08). These results highlight the need for novel treatment approaches in CHR-P. Future studies should consider the heterogeneity of this clinical population and prioritise stratification strategies and bespoke treatments.

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Glioblastoma (GBM) is the most prevalent malignant brain tumor with poor prognosis. Although chromatin intratumoral heterogeneity is a characteristic feature of GBM, most current studies are conducted at a single tumor site. To investigate the GBM-specific 3D genome organization and its heterogeneity, we conducted Hi-C experiments in 21 GBM samples from nine patients, along with three normal brain samples. We identified genome subcompartmentalization and chromatin interactions specific to GBM, as well as extensive intertumoral and intratumoral heterogeneity at these levels. We identified copy number variants (CNVs) and structural variations (SVs) and demonstrated how they disrupted 3D genome structures. SVs could not only induce enhancer hijacking but also cause the loss of enhancers to the same gene, both of which contributed to gene dysregulation. Our findings provide insights into the GBM-specific 3D genome organization and the intratumoral heterogeneity of this organization and open avenues for understanding this devastating disease.

Lipid homeostasis is critical to neuronal survival. ATP-binding cassette A (ABCA) proteins are lipid transporters associated with neurodegenerative diseases. How ABCA transporters regulate lipid homeostasis in neurodegeneration is an outstanding question. Here we report that theDrosophilaABCA protein engulfment ABC transporter in the ovary (Eato) regulates phagocytosis-dependent neurodegeneration by playing opposing roles in neurons and phagocytes: In neurons, Eato prevents dendrites and axons from being attacked by neighboring phagocytes; in phagocytes, Eato sensitizes the cell for detecting neurons as engulfment targets. Thus,Eatodeficiency in neurons alone causes phagocytosis-dependent neurite degeneration, but additionalEatoloss from phagocytes suppresses the neurite degeneration. Mechanistically, Eato functions by removing the eat-me signal phosphatidylserine from the cell surface in both neurons and phagocytes. Multiple human and worm ABCA homologs can rescueEatoloss in phagocytes but not in neurons, suggesting both conserved and cell type–specific activities of ABCA proteins. These results imply possible mechanisms of neuron-phagocyte interactions in neurodegenerative diseases.

Tissue stiffness plays a crucial role in regulating morphogenesis. The ability to measure and monitor the dynamic progression of tissue stiffness is important for generating and testing mechanistic hypotheses. Methods to measure tissue properties in vivo have been emerging but present challenges with spatial and temporal resolution especially in 3D, by their reliance on highly specialized equipment, and/or due to their invasive nature. Here, we introduce light sheet elastography, a noninvasive method that couples low-frequency shear waves with light sheet fluorescence microscopy by adapting commercially available instruments. With this method, we achieved in toto stiffness mapping of organ-stage mouse and zebrafish embryos at cellular resolution. Versatility of the method enabled time-lapse stiffness mapping during tissue remodeling and of the beating embryonic heart. This method expands the spectrum of tools available to biologists and presents opportunities for uncovering the mechanical basis of morphogenesis.

Predictions of tropical cyclone (TC) frequencies are hampered by insufficient knowledge of their natural variability in the past. A 30-m-long sediment core from the Great Blue Hole, a marine sinkhole offshore Belize, provides the longest available, continuous, and annually resolved TC-frequency record. This record expands our understanding, derived from instrumental monitoring (73 years), historical documentations (173 years), and paleotempestological records (2000 years), to the past 5700 years. A total of 694 event layers were identified. They display a distinct regional trend of increasing storminess in the southwestern Caribbean, which follows an orbitally driven shift in the Intertropical Convergence Zone. Superimposed short-term variations match Holocene climate intervals and originate from solar irradiance–controlled sea-surface temperature anomalies and climate phenomena modes. A 21st-century extrapolation suggests an unprecedented increase in TC frequency, attributable to the Industrial Age warming.

Aortic valve stenosis (AVS) is a progressive disease, wherein males more often develop valve calcification relative to females that develop valve fibrosis. Valvular interstitial cells (VICs) aberrantly activate to myofibroblasts during AVS, driving the fibrotic valve phenotype in females. Myofibroblasts further differentiate into osteoblast-like cells and produce calcium nanoparticles, driving valve calcification in males. We hypothesized that the lysine demethylase UTY (ubiquitously transcribed tetratricopeptide repeat containing Y-linked) decreases methylation uniquely in male VICs responding to nanoscale extracellular matrix cues to promote an osteoblast-like cell phenotype. Here, we describe a hydrogel biomaterial cell culture platform to interrogate how nanoscale cues modulate sex-specific methylation states in VICs activating to myofibroblasts and osteoblast-like cells. We found that UTY modulates the osteoblast-like cell phenotype in response to nanoscale cues uniquely in male VICs. Overall, we reveal a previously unidentified role of UTY in the regulation of calcification processes in males during AVS progression.

Bacterial populations experience chemical gradients in nature. However, most experimental systems either ignore gradients or fail to capture gradients in mechanically relevant contexts. Here, we use microfluidic experiments and biophysical simulations to explore how host-relevant shear flow affects antimicrobial gradients across communities of the highly resistant pathogenPseudomonas aeruginosa. We discover that flow patterns gradients of three chemically distinct antimicrobials: hydrogen peroxide, gentamicin, and carbenicillin. Without flow, resistantP. aeruginosacells generate local gradients by neutralizing all three antimicrobials through degradation or chemical modification. As flow increases, delivery overwhelms neutralization, allowing antimicrobials to penetrate deeper into bacterial populations. By imaging single cells across long microfluidic channels, we observe that upstream cells protect downstream cells, and protection is abolished in higher flow regimes. Together, our results reveal that physical flow can promote antimicrobial effectiveness, which could inspire the incorporation of flow into the discovery, development, and implementation of antimicrobials.

Oxygen plays a critical role in early neural development in brains, particularly before establishment of complete vasculature; however, it has seldom been investigated due to technical limitations. This study uses an in vitro human cerebral organoid model with multiomic analysis, integrating advanced microscopies and single-cell RNA sequencing, to monitor tissue oxygen tension during neural development. Results reveal a key period between weeks 4 and 6 with elevated intra-organoid oxygen tension, altered energy homeostasis, and rapid neurogenesis within the organoids. The timed oxygen tension elevation can be suppressed by hypoxia treatment or silencing of neuroglobin gene. This study provides insights into the role of oxygen in early neurogenesis from functional, genotypic, phenotypic, and proteomic aspects. These findings highlight the significance of the timed tissue oxygen tension elevation in neurogenesis and provide insights into the role of neuroglobin in neural development, with potential implications for understanding neurodegenerative diseases and therapeutic strategies.

Whether restoration actions achieve full ecological recovery is still debated. This is particularly controversial in the marine realm, where the success of restoration is mostly evaluated in terms of the short-term survival of transplanted organisms. In view of this, we combined population and trait-based approaches to explore the long-term effectiveness of active restoration of a key Mediterranean octocoral. For this purpose, an assemblage with restoredCorallium rubrumcolonies was monitored over 10 years and compared with a nearby reference site. Our results revealed growth of the transplanted colonies followed by a change in the functional structure (i.e., dominance and diversity of traits) of the restored assemblage. This change was related not only to the development of the coral but also to the arrival and/or increase of species with different traits. Overall, our findings provide an example of how active restoration of long-lived octocorals can be an effective tool for recovering high-diverse coralligenous assemblages at decadal timescales.

Invasive infections by encapsulated bacteria are the major cause of human morbidity and mortality. The liver resident macrophages, Kupffer cells, form the hepatic firewall to clear many encapsulated bacteria in the blood circulation but fail to control certain high-virulence capsule types. Here we report that the spleen is the backup immune organ to clear the liver-resistant serotypes ofStreptococcus pneumoniae(pneumococcus), a leading human pathogen. Asplenic mice failed to control the growth of the liver-resistant pneumococci in the blood circulation. Immunologic and genetic analyses identified splenic red pulp (RP) macrophages as the major phagocytes for bacterial clearance. Furthermore, the plasma natural antibodies against the cell wall phosphocholine and the complement system were necessary for RP macrophage–mediated immunity. These findings have provided a conceptual framework for the innate defense against blood bacterial infections, a mechanistic explanation for the hyper-susceptibility of asplenic individuals toS. pneumoniae, and a proof of concept for developing vaccines and therapeutic antibodies against encapsulated pathogens.

Intrabronchial delivery of therapeutic agents is critical to the treatment of respiratory diseases. Targeted delivery is demanded because of the off-target accumulation of drugs in normal lung tissues caused by inhalation and the limited motion dexterity of clinical bronchoscopes in tortuous bronchial trees. Herein, we developed microrobotic swarms consisting of magnetic hydrogel microparticles to achieve intrabronchial targeted delivery. Under programmed magnetic fields, the microgel particle swarms performed controllable locomotion and adaptative structure reconfiguration in tortuous and air-filled environments. The swarms were further integrated with imaging contrast agents for precise tracking under x-ray fluoroscopy and computed tomography imaging. Magnetic navigation of the swarms in an ex vivo lung phantom and in vivo delivery into deep branches of the bronchial trees were achieved. The on-demand reconfiguration of swarms for avoiding the microgel particles from entering nontarget bronchi and the precise delivery into tilted bronchi through climbing motion were validated.

Pancreatic cancer (PC) is a highly metastatic malignancy. More than 80% of patients with PC present with advanced-stage disease, preventing potentially curative surgery. The neuropeptide Y (NPY) system, best known for its role in controlling energy homeostasis, has also been shown to promote tumorigenesis in a range of cancer types, but its role in PC has yet to be explored. We show that expression of NPY andNPY1Rare up-regulated in mouse PC models and human patients with PC. Moreover, using the genetically engineered, autochthonous KPR172HC mouse model of PC, we demonstrate that pancreas-specific and whole-body knockout ofNpy1rsignificantly decreases metastasis to the liver. We identify that treatment with the NPY1R antagonist BIBO3304 significantly reduces KPR172HC migratory capacity on cell-derived matrices. Pharmacological NPY1R inhibition in an intrasplenic model of PC metastasis recapitulated the results of our genetic studies, with BIBO3304 significantly decreasing liver metastasis. Together, our results reveal that NPY/NPY1R signaling is a previously unidentified antimetastatic target in PC.

Recalcitrant biofilm infections pose a great challenge to human health. Micro- and nanorobots have been used to eliminate biofilm infections in hard-to-reach regions inside the body. However, applying antibiofilm robots under physiological conditions is limited by the conflicting demands of accessibility and driving force. Here, we introduce a liquid-bodied antibiofilm robot constructed by a dynamically cross-linked magnetic hydrogel. Leveraging the viscoelastic response of the robot enables it to adapt to complex surface topographies such as medical meshes and stents. Upon actuation, the robot can mechanically destroy the biofilm matrix, chemically deactivate bacterial cells, and collect disrupted biofilm debris. The robot’s antibiofilm performance is studied in vitro and demonstrated on a medical mesh and a biliary stent. Tracking and navigation under endoscopy and x-ray imaging in an ex vivo porcine bile duct are demonstrated. Last, in vivo antibiofilm treatment is conducted by indwelling infected stents into mice’s abdominal cavity and clearing the biofilm infection using the proposed robot.

To provide protection, anticipatory T cell–dependent immunity is reliant on the generation and maintenance of a naïve T cell repertoire, which is sufficiently diverse to ensure recognition of newly encountered antigens. Therefore, under steady-state conditions, a given individual needs to maintain a large pool of naïve T cells, ready to respond to potential threats. Here, we demonstrate that N-myc downstream-regulated gene 3 (Ndrg3) is essential for naïve T cell stability. Mice with T cell–specific Ndrg3 loss are lymphopenic, with reduced numbers of conventional T cells and natural killer T cells. We show that in the absence of Ndrg3, naïve CD8+ T cells exhibit high rates of both proliferation and apoptosis, phenotypes that could be partially rescued by transgenic expression of a high-avidity T cell receptor. Furthermore, Ndrg3-deficient cells were refractory to interleukin-4, resulting in reduced Eomes induction, and a decreased virtual memory population. Our study therefore identifies Ndrg3 as an unexpected, pleiotropic regulator of T cell homeostasis.

Lung cancer exhibits altered metabolism, influencing its response to radiation. To investigate the metabolic regulation of radiation response, we conducted a comprehensive, metabolic-wide CRISPR-Cas9 loss-of-function screen using radiation as selection pressure in human non–small cell lung cancer. Lipoylation emerged as a key metabolic target for radiosensitization, with lipoyltransferase 1 (LIPT1) identified as a top hit. LIPT1 covalently conjugates mitochondrial 2-ketoacid dehydrogenases with lipoic acid, facilitating enzymatic functions involved in the tricarboxylic acid cycle. Inhibiting lipoylation, either through genetic LIPT1 knockout or a lipoylation inhibitor (CPI-613), enhanced tumor control by radiation. Mechanistically, lipoylation inhibition increased 2-hydroxyglutarate, leading to H3K9 trimethylation, disrupting TIP60 recruitment and ataxia telangiectasia mutated (ATM)–mediated DNA damage repair signaling, impairing homologous recombination repair. In summary, our findings reveal a critical role of LIPT1 in regulating DNA damage and chromosome stability and may suggest a means to enhance therapeutic outcomes with DNA-damaging agents.

The emergence and rapid spread of multidrug-resistantBotrytis cinereastrains pose a great challenge to the quality and safety of agricultural products and the efficient use of pesticides. Previously unidentified fungicides and targets are urgently needed to combatB. cinerea–associated infections as alternative therapeutic options. In this study, the promising compound Z24 demonstrated efficacy against all tested plant pathogenic fungi. Thiamine thiazole synthase (Bcthi4) was identified as a target protein of Z24 by drug affinity responsive target stability (DARTS), cellular thermal shift assay (CETSA), and surface plasmon resonance (SPR) assays. Molecular docking and enzyme activity experiments have demonstrated that Z24 can affect the function of Bcthi4. Last, mechanistic studies show that Z24 inhibits thiamine biosynthesis by binding to Bcthi4 and induces up-regulation of alternative splicing [alternative 5′ splice site (A5SS)] of theBcthi4gene. In conclusion, by targeting Bcthi4, Z24 has the potential to be developed as a previously unidentified anti–B. cinereacandidate.

There is great interest in using genetically tractable organisms such asDrosophilato gain insights into the regulation and function of sleep. However, sleep phenotyping inDrosophilahas largely relied on simple measures of locomotor inactivity. Here, we present FlyVISTA, a machine learning platform to perform deep phenotyping of sleep in flies. This platform comprises a high-resolution closed-loop video imaging system, coupled with a deep learning network to annotate 35 body parts, and a computational pipeline to extract behaviors from high-dimensional data. FlyVISTA reveals the distinct spatiotemporal dynamics of sleep and wake-associated microbehaviors at baseline, following administration of the sleep-inducing drug gaboxadol, and with dorsal fan-shaped body drivers. We identify a microbehavior (“haltere switch”) exclusively seen during quiescence that indicates a deeper sleep stage. These results enable the rigorous analysis of sleep inDrosophilaand set the stage for computational analyses of microbehaviors in quiescent animals.

After an election, should election officials release a copy of each anonymous ballot? Some policy-makers have championed public disclosure to counter distrust, but others worry that it might undermine ballot secrecy. We introduce the term vote revelation to refer to the linkage of a vote on an anonymous ballot to the voter’s name in the public voter file and detail how such revelation could theoretically occur. Using the 2020 election in Maricopa County, Arizona, as a case study, we show that the release of individual ballot records would lead to no revelation of any vote choice for 99.83% of voters as compared to 99.95% under Maricopa’s current practice of reporting aggregate results by precinct and method of voting. Further, revelation is overwhelmingly concentrated among the few voters who cast provisional ballots or federal-only ballots. We discuss the potential benefits of transparency, compare remedies to reduce or eliminate privacy violations, and highlight the privacy-transparency trade-off inherent in all election reporting.

U6 small nuclear RNA (U6 snRNA), a critical spliceosome component primarily found in the nucleus, plays a vital role in RNA splicing. Our previous study, using the simian immunodeficiency virus (SIV) macaque model, revealed an increase of U6 snRNA in plasma extracellular vesicles (EVs) in acute retroviral infection. Given the limited understanding of U6 snRNA dynamics across cells and EVs, particularly in SIV infection, this research explores U6 snRNA trafficking and its association with splicing proteins in the nucleus, cytoplasm, and EVs. We observed a redistribution of U6 snRNA from the nucleus to EVs post-infection, accompanied by distinct protein profile changes and alterations in nucleic acid metabolism and spliceosome pathways. In addition, U6 machinery proteins changed in cells and EVs in a contrasting manner. The redistribution of U6 and related proteins we observed could be part of a viral strategy to redirect host splicing machinery, suggesting that U6 may have regulatory roles and be part of retroviral infection signature.

Duchenne muscular dystrophy (DMD) is a devastating X-linked disorder caused by dystrophin gene mutations. Despite recent advances in understanding the disease etiology and applying emerging treatment methodologies, glucocorticoid derivatives remain the only general therapeutic option that can slow disease development. However, the precise molecular mechanism of glucocorticoid action remains unclear, and there is still need for additional remedies to complement the treatment. Here, using single-nucleus RNA sequencing and spatial transcriptome analyses of human and mouse muscles, we investigated pathogenic features in patients with DMD and palliative effects of glucocorticoids. Our approach further illuminated the importance of proliferating satellite cells and revealed increased activity of a signal transduction pathway involving EZH2 in the patient cells. Subsequent administration of EZH2 inhibitors toDmdmutant mice resulted in improved muscle phenotype through maintaining the immune-suppressing effect but overriding the muscle weakness and fibrogenic effects exerted by glucocorticoids. Our analysis reveals pathogenic mechanisms that can be readily targeted by extant therapeutic options for DMD.

Timely detection of early atherosclerosis (AS) is crucial for improving cardiovascular outcomes, creating a growing demand for diagnostic tools that are simple, sensitive, and cost-effective. Here, we introduce a synthetic nanosensor for early AS detection that leverages the fluorescence and renal clearance properties of carbon quantum dots (CQDs). This nanosensor, designed to respond to the proteolytic activity of AS-associated dysregulated enzymes, entails CQDs as signal reporters to convert AS-associated proteolytic activity to fluorometric readings enabling a sensitive and cost-effective urine-based assay for early AS detection. Our findings demonstrated that the nanosensor provided distinct signals in atherosclerotic versus healthy mice at early AS stages, indicating its diagnostic potential. Moreover, toxicity tests showed no notable adverse effects, supporting its safety for diagnostic applications. This minimally invasive diagnostic approach could facilitate personalized therapy design and continuous efficacy assessment. It is expected that such a modular nanosensor platform can be integrated with simple urine tests to offer cost-effective detection of various diseases.

Aging involves the progressive accumulation of cellular damage, leading to systemic decline and age-related diseases. Despite advances in medicine, accurately predicting biological age (BA) remains challenging due to the complexity of aging processes and the limitations of current models. This study introduces a method for predicting BA using a deep neural network (DNN) based on pathways of steroidogenesis. We analyzed 22 steroids from 148 serum samples of individuals aged 20 to 73, using 98 samples for model training and 50 for validation. Our model reflects the often-overlooked fact that aging heterogeneity expands over time and uncovers sex-specific variations in steroidogenesis. This study leveraged key markers, including cortisol (COL), which underscore the role of stress-related and sex-specific steroids in aging. The resulting model establishes a biologically meaningful and robust framework for predicting BA across diverse datasets, offering fresh insights and supporting more targeted strategies in aging research and disease management.

The testis-specific BET protein BRDT structurally resembles the ubiquitous BRD4 and is misexpressed in cancer, and we show that BRDT misexpression may affect lung cancer progression. BRDT knockdown in lung cancer cells slowed tumor growth and prolonged survival in a xenograft model. Comparative characterization of PTEFb complex participation and chromatin binding indicates BRD4-redundant and BRD4-distinct BRDT functions. Unlike dual depletion, individual BRD4 or BRDT knockdown did not impair transcriptional responses to hypoxia in BRDT-expressing cells, consistent with redundant function. However, BRD4 depletion/BRDT complementation revealed that BRDT can also release paused RNA polymerase II independently of its bromodomains as we previously demonstrated not to be required for Pol II pause/release function of BRD4, underscoring the functional importance of the C-terminal domains in both BRD4 and BRDT and their potential as therapeutic targets in solid tumors. Based on this study, future investigations should explore BRD4-distinct BRDT functions and BRDT misexpression driving cancer pathogenesis.

Anthropogenically forced climate change signals are emerging from the noise of internal variability in observations, and the impacts on society are growing. For decades, Climate or Earth System Models have been predicting how these climate change signals will unfold. While challenges remain, given the growing forced trends and the lengthening observational record, the climate science community is now in a position to confront the signals, as represented by historical trends, in models with observations. This review covers the state of the science on the ability of models to represent historical trends in the climate system. It also outlines robust procedures that should be used when comparing modeled and observed trends and how to move beyond quantification into understanding. Finally, this review discusses cutting-edge methods for identifying sources of discrepancies and the importance of future confrontations.

Searching for land refugia becomes imperative for human survival during the hypothetical sixth mass extinction. Studying past comparable crises can offer insights, but there is no fossil evidence of diverse megafloral ecosystems surviving the largest Phanerozoic biodiversity crisis. Here, we investigated palynomorphs, plant, and tetrapod fossils from the Permian-Triassic South Taodonggou Section in Xinjiang, China. Our fossil records, calibrated by a high-resolution age model, reveal the presence of vibrant regional gymnospermous forests and fern fields, while marine organisms experienced mass extinction. This refugial vegetation was crucial for nourishing the substantial influx of surviving animals, thereby establishing a diverse terrestrial ecosystem approximately 75,000 years after the mass extinction. Our findings contradict the widely held belief that restoring terrestrial ecosystem functional diversity to pre-extinction levels would take millions of years. Our research indicates that moderate hydrological fluctuations throughout the crisis sustained this refugium, likely making it one of the sources for the rapid radiation of terrestrial life in the early Mesozoic.

Environmental influences on traits and associated transgenerational epigenetic inheritance have widespread implications but remain controversial and underlying mechanisms poorly understood. We introduce long-term environmental induction experiments on alternative diets inPristionchus pacificus, a nematode exhibiting mouth-form plasticity including predation, by propagating 110 isogenic lines for 101 generations with associated food-reversal experiments. We found dietary induction and subsequent transgenerational inheritance of the predatory morph and identified a role of ubiquitin ligase EBAX-1/ZSWIM8 in this process.Ppa-ebax-1mutants are transgenerational inheritance defective, andPpa-EBAX-1 destabilizes the clustered microRNA familymiR-2235a/miR-35.Deletions of a cluster of 44 identicalmiR-2235acopies resulted in precocious and extended transgenerational inheritance of the predatory morph. These findings indicate that EBAX-1/ZSWIM8 destabilizes miRNAs, resulting in transgenerational inheritance, suggesting a role for target-directed miRNA degradation.

DNA nanostructures are typically assembled by thermal annealing in buffers containing magnesium. We demonstrate the assembly of DNA nanostructures at constant temperatures ranging from 4° to 50°C in solutions containing different counterions. The choice of counterions and the assembly temperature influence the isothermal assembly of several DNA motifs and designed three-dimensional DNA crystals. Molecular dynamics simulations show more fluctuations of the DNA structure in select monovalent ions (Na+and K+) compared to divalent ions (Mg2+and Ca2+). A key highlight is the successful assembly of DNA motifs in nickel-containing buffer at temperatures below 40°C, otherwise unachievable at higher temperatures or using an annealing protocol. DNA nanostructures isothermally assembled in different ions do not affect the viability of fibroblasts, myoblasts, and myotubes or the immune response in myoblasts. The use of ions other than the typically used magnesium holds key potential in biological and materials science applications that require minimal amounts of magnesium.

Stretched-exponential protein refolding kinetics, first observed decades ago, were attributed to a nonnative ensemble of structures with parallel, non-interconverting folding pathways. However, the structural origin of the large energy barriers preventing interconversion between these folding pathways is unknown. Here, we combine simulations with limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS) to study the protein phosphoglycerate kinase (PGK). Simulations recapitulate its stretched-exponential folding kinetics and reveal that misfolded states involving changes of entanglement underlie this behavior: either formation of a nonnative, noncovalent lasso entanglement or failure to form a native entanglement. These misfolded states act as kinetic traps, requiring extensive unfolding to escape, which results in a distribution of free energy barriers and pathway partitioning. Using LiP-MS and XL-MS, we propose heterogeneous structural ensembles consistent with these data that represent the potential long-lived misfolded states PGK populates. This structural and energetic heterogeneity creates a hierarchy of refolding timescales, explaining stretched-exponential kinetics.

The real-time monitoring of health conditions of humans is a long-lasting topic, but there are two major challenges. First, many biomedical applications accept only implanted sensors. Second, tissue-like soft sensors often suffer from viscoelasticity-induced signal drift, causing inaccurate measurements. Here, we report a wireless and drift-free sensory system enabled by a low-creep polyelectrolyte elastomer. The system consists of the iontronic pressure sensors incorporating inductance-capacitance (LC) oscillators, exhibiting combined low drift ratio, highQfactor, high robustness to interferences, and wide-range measurement, superior to other capacitive sensors using regular dielectrics or ionogels. We have recorded 14-day orthodontic loads of two subjects using the system, showing pressure decreasing from 300 to 50 kPa and torque from 12.5 to 0.5 N·mm. The wireless, drift-free sensory system may be extended to other implants for long-term and accurate sensing.

Driven by boosting demands for sustainable energy, highly conductive hydroxide exchange membranes (HEMs) are urgently required in electrochemical conversion devices. The hydrogen bonds shorter than 2.5 angstrom are expected to accelerate the ion transport. However, short hydrogen bonds (SHBs) can hardly form naturally because of the electron-withdrawing capability of O atom, which impedes its applications in water-mediated ion transport. This work develops an interlayer confinement strategy to construct SHB networks in a two-dimensional (2D) nanocapillary assembled by bismuth oxyiodide (BiOI) nanosheets and boost the ionic conductivity of HEMs. With confined nanochannels and adjustable hydrophilic groups in BiOI-based HEMs, the number of SHBs increases by 12 times, creating a shortcut for the Grotthuss-type anion transport, which in turn affords a high ionic conductivity of 168 millisiemens per centimeter at 90°C, higher than polymeric HEM and 2D-based HEM. This work demonstrates the facile approach to generating SHB networks in 2D capillaries and opens a promising avenue to developing advanced HEMs.

NALCN (sodium leak channel, nonselective) is vital for regulating electrical activity in neurons and other excitable cells, and mutations in the channel or its auxiliary proteins lead to severe neurodevelopmental disorders. Here, we show that the neuronal SNARE (solubleN-ethylmaleimide–sensitive factor attachment protein receptors) complex proteins syntaxin and SNAP25 (synaptosome-associated protein 25), which enable synaptic transmission in the nervous system, inhibit the activity of the NALCN channel complex in both heterologous systems and primary neurons. The existence of this interaction suggests that the neurotransmitter release machinery can regulate electrical signaling directly and therefore modulate the threshold for its own activity. We further find that reduction of NALCN currents is sufficient to promote cell survival in syntaxin-depleted cells. This suggests that disinhibited NALCN may cause the puzzling phenomenon of rapid neuronal cell death in the absence of syntaxin. This interaction could offer opportunities for future drug development against genetic diseases linked to both NALCN- and SNARE protein–containing complexes.

Astrocytes, traditionally viewed as supportive cells within the central nervous system (CNS), are now recognized as dynamic regulators of neural signaling and homeostasis. They actively engage in synaptic transmission and brain health by releasing gliotransmitters such as glutamate, GABA, ATP, adenosine, lactate, andd-serine. Astrocytes also play a critical role in ion homeostasis and immune response through cytokine modulation and reactive oxygen species regulation. In pathological states, astrocytes can become reactive, contributing to neurodegeneration through dysregulated gliotransmitter release and metabolic dysfunction. Recently developed molecular and pharmacological tools allow the exploration of astrocytic response to injury and its influence on neuronal function. This review explores the multifaceted roles of astrocytes in health and disease, emphasizing sensory and motor functions as well as various neurological and psychiatric disorders. Understanding astrocyte-neuron signaling in health and disease provides crucial insights into their dual roles, offering novel avenues for therapeutic interventions in CNS disorders.

Life on this planet is heavily influenced by light, the most critical external environmental factor. Mammals perceive environmental light mainly through three types of photoreceptors in the retina—rods, cones, and intrinsically photosensitive retinal ganglion cells (ipRGCs). The latest discovered ipRGCs are particularly sensitive to short-wavelength light and have a unique phototransduction mechanism, compared with rods and cones. Piles of evidence suggest that ipRGCs mediate a series of light-regulated physiological functions such as circadian rhythms, sleep, metabolic homeostasis, mood, development, and higher cognitions, collectively known as non-image-forming vision. Recent advances in systems neuroscience, driven by modern neural circuit tools, have illuminated the structure and function of the neural pathways connecting the retina to subcortical regions, highlighting their involvement in an array of non-image-forming functions. Here we review key discoveries and recent progress regarding the neural circuit mechanisms employed by ipRGCs to regulate diverse biological functions and provide insights into unresolved scientific questions in this area.

The synapse is polarized and highly compartmentalized on both its pre- and postsynaptic sides. The compartmentalization of synaptic vesicles, as well as vesicle releasing and recycling machineries, allows neurotransmitters to be released with precisely controlled timing, speed, and amplitude. The compartmentalized and clustered organization of neurotransmitter receptors and their downstream signaling enzymes allows neuronal signals to be properly received and amplified. Synaptic adhesion molecules also form clustered assemblies to align pre- and postsynaptic subcompartments for synaptic formation, stability, and transmission. Recent studies indicate that such synaptic and subsynaptic compartmentalized organizations are formed via phase separation. This review discusses how such condensed subsynaptic compartments may form and function in the context of synapse formation and plasticity. We discuss how phase separation allows for the formation of multiple distinct condensates on both sides of a synapse and how such condensates communicate with each other. We also highlight how proteins display unique properties in condensed phases compared to the same proteins in dilute solutions.

Social behaviors, including parental care, mating, and fighting, all depend on the hormonal milieu of an organism. Decades of work highlighted estrogen as a key hormonal controller of social behaviors, exerting its influence primarily through binding to estrogen receptor alpha (Esr1). Recent technological advances in chemogenetics, optogenetics, gene editing, and transgenic model organisms have allowed for a detailed understanding of the neuronal subpopulations and circuits for estrogen action across Esr1-expressing interconnected brain regions. Focusing on rodent studies, in this review we examine classical and contemporary research demonstrating the multifaceted role of estrogen and Esr1 in regulating social behaviors in a sex-specific and context-dependent manner. We highlight gaps in knowledge, particularly a missing link in the molecular cascade that allows estrogen to exert such a diverse behavioral repertoire through the coordination of gene expression changes. Understanding the molecular and cellular basis of Esr1’s action in social behaviors provides insights into the broader mechanisms of hormone-driven behavior modulation across the lifespan.

During rest and sleep, the brain processes information through replay, reactivating neural patterns linked to past events and facilitating the exploration of potential future scenarios. This review summarizes recent advances in understanding human replay and its biomarker, sharp-wave ripples (SPW-Rs). We explore detection methods and connect insights from rodent studies. The review highlights unique aspects of human replay in internal cognition such as prioritizing past experiences for offline learning, generating hypothesized solutions to current problems, and factorizing structural representations for future generalization. We also examine the characteristics of SPW-Rs in humans, including their distribution along the hippocampal longitudinal axis, their widespread brain activations, and their influence on internal cognitive processes. Finally, we emphasize the need for improved methodologies and technologies to advance our understanding of cognitive processes during rest and sleep.

Major depressive disorder and treatment-resistant depression are significant worldwide health problems that need new therapies. The success of the anesthetic ketamine as an antidepressant is well known. It is less widely known that several other anesthetic agents have also shown antidepressant effects. These include nitrous oxide, propofol, isoflurane, sevoflurane, dexmedetomidine, and xenon. We review clinical and basic science investigations that have studied the therapeutic value of these anesthetics for treating depression. We propose potential neurophysiological mechanisms underlying the antidepressant effects of anesthetics by combining our understanding of how anesthetics modulate brain dynamics to alter arousal states, current theories of depression pathophysiology, and findings from other depression treatment modalities.

Medulloblastoma is the most common pediatric brain cancer and is broadly categorized into four molecular subgroups. Understanding the cell origins of medulloblastoma is crucial for preventing tumor formation and relapse. Recent single-cell transcriptomics studies have identified the potential cell lineage vulnerabilities and mechanisms underpinning malignant transformation in medulloblastoma. Emerging evidence suggests that genetic-epigenetic alterations specific to each subgroup lead to a lineage-specific stall in the neural developmental program and subsequent tumorigenesis. We discuss the putative cells of origin, plasticity, and heterogeneity within medulloblastoma subgroups and delve into the genetic and epigenetic changes that predispose cells to transformation. Additionally, we review the current insights into how cerebellar stem/progenitor cells and lineage plasticity impact medulloblastoma pathogenesis and highlight recent therapeutic advances targeting specific oncogenic vulnerabilities in this malignancy.

Cognition unfolds dynamically over flexible timescales. A major goal of the field is to understand the computational and neurobiological principles that enable this flexibility. Here, we argue that the neurobiology of timing provides a platform for tackling these questions. We begin with an overview of proposed coding schemes for the representation of elapsed time, highlighting their computational properties. We then leverage the one-dimensional and unidirectional nature of time to highlight common principles across these coding schemes. These principles facilitate a precise formulation of questions related to the flexible control, variability, and calibration of neural dynamics. We review recent work that demonstrates how dynamical systems analysis of thalamocortical population activity in timing tasks has provided fundamental insights into how the brain calibrates and flexibly controls neural dynamics. We conclude with speculations about the architectural biases and neural substrates that support the control and calibration of neural dynamics more generally.

Locomotion, like all behaviors, possesses an inherent flexibility that allows for the scaling of movement kinematic features, such as speed and vigor, in response to an ever-changing external world and internal drives. This flexibility is embedded in the organization of the spinal locomotor circuits, which encode and decode commands from the brainstem and proprioceptive feedback. This review highlights our current understanding of the modular organization of these locomotor circuits and how this modularity endows them with intrinsic mechanisms to adjust speed and vigor, thereby contributing to the flexibility of locomotor movements.

The twenty-first century has brought forth a deluge of theories and data shedding light on the neural mechanisms of motivated behavior. Much of this progress has focused on dopaminergic dynamics, including their signaling properties (how do they vary with expectations and outcomes?) and their downstream impacts in target regions (how do they affect learning and behavior?). In parallel, the basal ganglia have been elevated from their original implication in motoric function to a canonical circuit facilitating the initiation, invigoration, and selection of actions across levels of abstraction, from motor to cognitive operations. This review considers how striatal D1 and D2 opponency allows animals to perform cost-benefit calculations across multiple scales: locally, whether to select a given action, and globally, whether to engage a particular corticostriatal circuit for guiding behavior. An emerging understanding of such functions reconciles seemingly conflicting data and has implications for neuroscience, psychology, behavioral economics, and artificial intelligence.

It is a common view that the intricate array of specialized domains in the ventral visual pathway is innately prespecified. What this review postulates is that it is not. We explore the origins of domain specificity, hypothesizing that the adult brain emerges from an interplay between a domain-general map-based architecture, shaped by intrinsic mechanisms, and experience. We argue that the most fundamental innate organization of cortex in general, and not just the visual pathway, is a map-based topography that governs how the environment maps onto the brain, how brain areas interconnect, and ultimately, how the brain processes information.

Deep brain stimulation (DBS), a method in which electrical stimulation is delivered to specific areas of the brain, is an effective treatment for managing symptoms of a number of neurological and neuropsychiatric disorders. Clinical access to neural circuits during DBS provides an opportunity to study the functional link between neural circuits and behavior. This review discusses how the use of DBS in Parkinson's disease and dystonia has provided insights into the brain networks and physiological mechanisms that underlie motor control. In parallel, insights from basic science about how patterns of electrical stimulation impact plasticity and communication within neural circuits are transforming DBS from a therapy for treating symptoms to a therapy for treating circuits, with the goal of training the brain out of its diseased state.

Over 40% of the human genome is composed of retrotransposons, DNA species that hold the potential to replicate via an RNA intermediate and are evolutionarily related to retroviruses. Retrotransposons are most studied for their ability to jump within a genome, which can cause DNA damage and novel insertional mutations. Retrotransposon-encoded products, including viral-like proteins, double-stranded RNAs, and extrachromosomal circular DNAs, can also be potent activators of the innate immune system. A growing body of evidence suggests that retrotransposons are activated in age-related neurodegenerative disorders and that such activation causally contributes to neurotoxicity. Here we provide an overview of retrotransposon biology and outline evidence of retrotransposon activation in age-related neurodegenerative disorders, with an emphasis on those involving TAR-DNA binding protein-43 (TDP-43) and tau. Studies to date provide the basis for ongoing clinical trials and hold promise for innovative strategies to ameliorate the adverse effects of retrotransposon dysregulation in neurodegenerative disorders.

Ant physiology has been fashioned by 100 million years of social evolution. Ants perform many sophisticated social and collective behaviors yet possess nervous systems similar in schematic and scale to that of the fruit fly Drosophila melanogaster, a popular solitary model organism. Ants are thus attractive complementary subjects to investigate adaptations pertaining to complex social behaviors that are absent in flies. Despite research interest in ant behavior and the neurobiological foundations of sociality more broadly, our understanding of the ant nervous system is incomplete. Recent technical advances have enabled cutting-edge investigations of the nervous system in a fashion that is less dependent on model choice, opening the door for mechanistic social insect neuroscience. In this review, we revisit important aspects of what is known about the ant nervous system and behavior, and we look forward to how functional circuit neuroscience in ants will help us understand what distinguishes solitary animals from highly social ones.

The cochlear implant (CI) is considered the most successful neuroprosthesis as it enables speech comprehension in the majority of the million otherwise deaf patients. In hearing by electrical stimulation of the auditory nerve, the broad spread of current from each electrode acts as a bottleneck that limits the transfer of sound frequency information. Hence, there remains a major unmet medical need for improving the quality of hearing with CIs. Recently, optogenetic stimulation of the cochlea has been suggested as an alternative approach for hearing restoration. Cochlear optogenetics promises to transfer more sound frequency information, hence improving hearing, as light can conveniently be confined in space to activate the auditory nerve within smaller tonotopic ranges. In this review, we discuss the latest experimental and technological developments of optogenetic hearing restoration and outline remaining challenges en route to clinical translation.

The zebrafish visual system has become a paradigmatic preparation for behavioral and systems neuroscience. Around 40 types of retinal ganglion cells (RGCs) serve as matched filters for stimulus features, including light, optic flow, prey, and objects on a collision course. RGCs distribute their signals via axon collaterals to 12 retinorecipient areas in forebrain and midbrain. The major visuomotor hub, the optic tectum, harbors nine RGC input layers that combine information on multiple features. The retinotopic map in the tectum is locally adapted to visual scene statistics and visual subfield–specific behavioral demands. Tectal projections to premotor centers are topographically organized according to behavioral commands. The known connectivity in more than 20 processing streams allows us to dissect the cellular basis of elementary perceptual and cognitive functions. Visually evoked responses, such as prey capture or loom avoidance, are controlled by dedicated multistation pathways that—at least in the larva—resemble labeled lines. This architecture serves the neuronal code's purpose of driving adaptive behavior.

The activity patterns of grid cells form distinctively regular triangular lattices over the explored spatial environment and are largely invariant to visual stimuli, animal movement, and environment geometry. These neurons present numerous fascinating challenges to the curious (neuro)scientist: What are the circuit mechanisms responsible for creating spatially periodic activity patterns from the monotonic input-output responses of single neurons? How and why does the brain encode a local, nonperiodic variable—the allocentric position of the animal—with a periodic, nonlocal code? And, are grid cells truly specialized for spatial computations? Otherwise, what is their role in general cognition more broadly? We review efforts in uncovering the mechanisms and functional properties of grid cells, highlighting recent progress in the experimental validation of mechanistic grid cell models, and discuss the coding properties and functional advantages of the grid code as suggested by continuous attractor network models of grid cells.

It has long been argued that only humans could produce and understand language. But now, for the first time, artificial language models (LMs) achieve this feat. Here we survey the new purchase LMs are providing on the question of how language is implemented in the brain. We discuss why, a priori, LMs might be expected to share similarities with the human language system. We then summarize evidence that LMs represent linguistic information similarly enough to humans to enable relatively accurate brain encoding and decoding during language processing. Finally, we examine which LM properties—their architecture, task performance, or training—are critical for capturing human neural responses to language and review studies using LMs as in silico model organisms for testing hypotheses about language. These ongoing investigations bring us closer to understanding the representations and processes that underlie our ability to comprehend sentences and express thoughts in language.

Predictive processing is a computational framework that aims to explain how the brain processes sensory information by making predictions about the environment and minimizing prediction errors. It can also be used to explain some of the key symptoms of psychotic disorders such as schizophrenia. In recent years, substantial advances have been made in our understanding of the neuronal circuitry that underlies predictive processing in cortex. In this review, we summarize these findings and how they might relate to psychosis and to observed cell type–specific effects of antipsychotic drugs. We argue that quantifying the effects of antipsychotic drugs on specific neuronal circuit elements is a promising approach to understanding not only the mechanism of action of antipsychotic drugs but also psychosis. Finally, we outline some of the key experiments that should be done. The aims of this review are to provide an overview of the current circuit-based approaches to psychosis and to encourage further research in this direction.

Auditory processing in mammals begins in the peripheral inner ear and extends to the auditory cortex. Sound is transduced from mechanical stimuli into electrochemical signals of hair cells, which relay auditory information via the primary auditory neurons to cochlear nuclei. Information is subsequently processed in the superior olivary complex, lateral lemniscus, and inferior colliculus and projects to the auditory cortex via the medial geniculate body in the thalamus. Recent advances have provided valuable insights into the development and functioning of auditory structures, complementing our understanding of the physiological mechanisms underlying auditory processing. This comprehensive review explores the genetic mechanisms required for auditory system development from the peripheral cochlea to the auditory cortex. We highlight transcription factors and other genes with key recurring and interacting roles in guiding auditory system development and organization. Understanding these gene regulatory networks holds promise for developing novel therapeutic strategies for hearing disorders, benefiting millions globally.

The cerebellum has a well-established role in controlling motor functions, including coordination, posture, and the learning of skilled movements. The mechanisms for how it carries out motor behavior remain under intense investigation. Interestingly though, in recent years the mechanisms of cerebellar function have faced additional scrutiny since nonmotor behaviors may also be controlled by the cerebellum. With such complexity arising, there is now a pressing need to better understand how cerebellar structure, function, and behavior intersect to influence behaviors that are dynamically called upon as an animal experiences its environment. Here, we discuss recent experimental work that frames possible neural mechanisms for how the cerebellum shapes disparate behaviors and why its dysfunction is catastrophic in hereditary and acquired conditions—both motor and nonmotor. For these reasons, the cerebellum might be the ideal therapeutic target.

Since its recent discovery, the meningeal lymphatic system has reshaped our understanding of central nervous system (CNS) fluid exchange, waste clearance, immune cell trafficking, and immune privilege. Meningeal lymphatics have also been demonstrated to functionally modify the outcome of neurological disorders and their responses to treatment, including brain tumors, inflammatory diseases such as multiple sclerosis, CNS injuries, and neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. In this review, we discuss recent evidence of the contribution of meningeal lymphatics to neurological diseases, as well as the available experimental methods for manipulating meningeal lymphatics in these conditions. Finally, we also provide a discussion of the pressing questions and challenges in utilizing meningeal lymphatics as a prime target for CNS therapeutic intervention and possibly drug delivery for brain disorders.

The hippocampus is critical for memory and spatial navigation. The ability to map novel environments, as well as more abstract conceptual relationships, is fundamental to the cognitive flexibility that humans and other animals require to survive in a dynamic world. In this review, we survey recent advances in our understanding of how this flexibility is implemented anatomically and functionally by hippocampal circuitry, during both active exploration (online) and rest (offline). We discuss the advantages and limitations of spike timing–dependent plasticity and the more recently discovered behavioral timescale synaptic plasticity in supporting distinct learning modes in the hippocampus. Finally, we suggest complementary roles for these plasticity types in explaining many-shot and single-shot learning in the hippocampus and discuss how these rules could work together to support the learning of cognitive maps.

To perform computations with the efficiency necessary for animal survival, neocortical microcircuits must be capable of reconfiguring in response to experience, while carefully regulating excitatory and inhibitory connectivity to maintain stable function. This dynamic fine-tuning is accomplished through a rich array of cellular homeostatic plasticity mechanisms that stabilize important cellular and network features such as firing rates, information flow, and sensory tuning properties. Further, these functional network properties can be stabilized by different forms of homeostatic plasticity, including mechanisms that target excitatory or inhibitory synapses, or that regulate intrinsic neuronal excitability. Here we discuss which aspects of neocortical circuit function are under homeostatic control, how this homeostasis is realized on the cellular and molecular levels, and the pathological consequences when circuit homeostasis is impaired. A remaining challenge is to elucidate how these diverse homeostatic mechanisms cooperate within complex circuits to enable them to be both flexible and stable.

Seeing in three dimensions is a major property of the visual system in mammals. The circuit underlying this property begins in the retina, from which retinal ganglion cells (RGCs) extend to the same or opposite side of the brain. RGC axons decussate to form the optic chiasm, then grow to targets in the thalamus and midbrain, where they synapse with neurons that project to the visual cortex. Here we review the cellular and molecular mechanisms of RGC axonal growth cone guidance across or away from the midline via receptors to cues in the midline environment. We present new views on the specification of ipsi- and contralateral RGC subpopulations and factors implementing their organization in the optic tract and termination in subregions of their targets. Lastly, we describe the functional and behavioral aspects of binocular vision, focusing on the mouse, and discuss recent discoveries in the evolution of the binocular circuit.

The intricate network of the brain's neurons and synapses poses unparalleled challenges for research, distinct from other biological studies. This is particularly true when dissecting how neurons and their functional units work at a cell biological level. While traditional microscopy has been foundational, it was unable to reveal the deeper complexities of neural interactions. However, an imaging renaissance has transformed our capabilities. Advancements in light and electron microscopy, combined with correlative imaging, now achieve unprecedented resolutions, uncovering the most nuanced neural structures. Maximizing these tools requires more than just technical proficiency. It is crucial to align research aims, allocate resources wisely, and analyze data effectively. At the heart of this evolution is interdisciplinary collaboration, where various experts come together to translate detailed imagery into significant biological insights. This review navigates the latest developments in microscopy, underscoring both the promise of and prerequisites for bending this powerful tool set to understanding neuronal cell biology.

In the natural world, animals make decisions on an ongoing basis, continuously selecting which action to undertake next. In the lab, however, the neural bases of decision processes have mostly been studied using artificial trial structures. New experimental tools based on the genetic toolkit of model organisms now make it experimentally feasible to monitor and manipulate neural activity in small subsets of neurons during naturalistic behaviors. We thus propose a new approach to investigating decision processes, termed reverse neuroethology. In this approach, experimenters select animal models based on experimental accessibility and then utilize cutting-edge tools such as connectomes and genetically encoded reagents to analyze the flow of information through an animal's nervous system during naturalistic choice behaviors. We describe how the reverse neuroethology strategy has been applied to understand the neural underpinnings of innate, rapid decision making, with a focus on defensive behavioral choices in the vinegar fly Drosophila melanogaster.

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How neurons detect the direction of motion is a prime example of neural computation: Motion vision is found in the visual systems of virtually all sighted animals, it is important for survival, and it requires interesting computations with well-defined linear and nonlinear processing steps—yet the whole process is of moderate complexity. The genetic methods available in the fruit fly Drosophila and the charting of a connectome of its visual system have led to rapid progress and unprecedented detail in our understanding of how neurons compute the direction of motion in this organism. The picture that emerged incorporates not only the identity, morphology, and synaptic connectivity of each neuron involved but also its neurotransmitters, its receptors, and their subcellular localization. Together with the neurons’ membrane potential responses to visual stimulation, this information provides the basis for a biophysically realistic model of the circuit that computes the direction of visual motion.

All mammalian cell membranes contain cholesterol to maintain membrane integrity. The transport of this hydrophobic lipid is mediated by lipoproteins. Cholesterol is especially enriched in the brain, particularly in synaptic and myelin membranes. Aging involves changes in sterol metabolism in peripheral organs and also in the brain. Some of those alterations have the potential to promote or to counteract the development of neurodegenerative diseases during aging. Here, we summarize the current knowledge of general principles of sterol metabolism in humans and mice, the most widely used model organism in biomedical research. We discuss changes in sterol metabolism that occur in the aged brain and highlight recent developments in cell type–specific cholesterol metabolism in the fast-growing research field of aging and age-related diseases, focusing on Alzheimer's disease. We propose that cell type–specific cholesterol handling and the interplay between cell types critically influence age-related disease processes.

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AbstractParkinson’s disease is characterized, in part, by hypoactivity of direct pathway inhibitory projections from striatum to the globus pallidus internus (GPi) and indirect pathway inhibitory projections from globus pallidus externus (GPe) to the subthalamic nucleus (STN). In people with Parkinson’s disease (n=32), we explored the potential use of intracranial stimulation for eliciting long-term potentiation (LTP) of these underactive pathways to produce improvement of symptoms that persists beyond stimulation cessation.During GPi deep brain stimulation (DBS) surgery, we found strong evidence (p<.05; BF10>10) of increased amplitudes of hand movements and striato-GPi evoked potentials before versus after high-frequency microstimulation. In a small sample of outpatients with sensing-enabled GPi-DBS, we found anecdotal evidence (p<.10; BF10>1) of improved hand movements and attenuated beta frequency oscillations. In STN, enduring behavioural effects, potentiation of GPe-STN projections (intraoperative), and decreases to beta oscillations (extraoperative) were not observed.Our findings support that LTP-like effects in GPi may produce motor improvements that extend beyond stimulation cessation, while the lack of effects in STN suggests the need for optimizing stimulation paradigms for effective LTP induction. These findings nevertheless highlight the potential of LTP-based strategies for sustained therapeutic benefits, which may be useful for mitigating DBS side-effects and optimizing battery usage.

AbstractPatients with anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis, often present with severe psychiatric symptoms, yet the neuropathological mechanisms underlying their cognitive deficits remain insufficiently understood. In this study, we constructed an animal model using anti-NMDAR IgG purified from the serum of patients with anti-NMDAR encephalitis, and we used IgG obtained from healthy individuals as a control. Daily administration of anti-NMDAR IgG into the medial prefrontal cortex (mPFC) of mice for 7 days resulted in cognitive impairments resembling clinical symptoms, which spontaneously resolved 30 days after discontinuing the injections.Immunohistochemical staining and electrophysiological testing of parvalbumin neurons in the mPFC treated with anti-NMDAR IgG revealed significant cellular morphological damage, reduced excitability, synaptic dysfunction and a loss of NMDAR antagonist-induced gamma oscillations. Application of optogenetic and pharmacogenetic techniques to activate parvalbumin neurons in the mPFC successfully reversed the cognitive impairments observed in the anti-NMDAR-IgG-treated mice. Single-cell sequencing of anti-NMDAR-IgG-treated parvalbumin neurons identified differentially expressed genes and pathways related to synapses and neuronal development, offering potential targets for therapeutic intervention. Additionally, we showed that these alterations in parvalbumin neurons were not confined to the mPFC, as similar changes were detected in the hippocampus after anti-NMDAR IgG injections.In summary, our findings elucidate distinct alterations in parvalbumin neurons during the pathogenesis of anti-NMDAR encephalitis, providing preclinical rationale for exploring approaches to modulate parvalbumin neuronal function to treat anti-NMDAR encephalitis.

AbstractIschemic strokes disrupt brain networks, leading to remote effects in key regions like the thalamus, a critical hub for brain functions. However, non-invasive methods to quantify these remote consequences still need to be explored. This study aimed to demonstrate that MRI-derived R2* changes can capture iron accumulation linked with inflammation secondary to stroke-induced disconnection.In order to link remote R2* changes to stroke-induced disconnection, we first conducted a secondary analysis of 156 prospectively included stroke patients who underwent MRI at baseline and 1-year follow-up. We mapped fibers disconnected by baseline infarcts to compare the R2* changes over 1 year according to the disconnectivity status in specific thalamic nuclei groups. We also identified the variables associated with elevated R2* at 1 year in a multivariate context through linear regressions. In parallel, to understand the biological underpinning of the remote R2* changes, we set up a translational mouse model through photothrombotic induction of focal cortical infarcts or sham procedures in 110 C57BL/6J mice. We explored the mice through combinations of in vivo MRI at 72h, 2-, 4-, and 8-weeks, histology, qPCR for gene expression, mass spectrometry for iron concentration quantification, and additional ex vivo high-resolution diffusion tensor imaging.In stroke patients, we found a significant increase of R2* within severely disconnected medial and lateral thalamic nuclei groups from baseline to 1 year. At the same time, no change occurred if these structures were not disconnected. We also showed that the disconnectivity status at baseline was significantly associated with R2* at follow-up, independently from confounders, establishing a direct and independent relationship between baseline disconnection and the subsequent R2* increase within the associated locations. In mice, we recapitulated the patients’ conditions by observing increased R2* in the stroke groups, specifically within the disconnected thalamic nuclei. Such remote and focal R2* changes peaked at 2 weeks, preceding and correlating with longer-term atrophy at 8 weeks. We established that the remote R2* increase was spatially and temporally correlated with a significant increase of chemically determined iron load bound to ferritin within activated microglial cells.This study provides critical evidence that R2* is a sensitive marker of inflammation secondary to network disconnection, potentially informing future neuroprotective strategies targeting remote brain regions after stroke.

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AbstractAfter stroke, upper extremity (UE) motor recovery may be mediated in part by transcallosal projections between hemispheres. The interhemispheric competition model posits that transcallosal inhibition (TI) from the contralesional hemisphere is abnormally strengthened following stroke and interferes with motor recovery. This model has recently been questioned.In this longitudinal study, we aimed to definitively confirm or refute a maladaptive role of contralesional TI in subacute motor recovery.We assessed 30 mild-to-moderately impaired subjects over the six months following ischemic stroke. We tracked contralesional TI and motor functions in the proximal and distal segments of the paretic UE. We used transcranial magnetic stimulation to examine the ipsilateral silent period (iSP) in an arm and hand muscle. We used quantitative and clinical testing to examine deficits in muscle strength, motor control, and individuation; UE segmental impairment; and UE activity limitation. We assessed the relationships of contralesional TI to motor functions in the subacute period.Despite recovery of most motor functions in the proximal and distal UE, contralesional TI was largely static and unrelated to recovery of any motor function. There were inconsistent associations between stronger TI, less hand impairment, and less activity limitation in the subacute period overall.We found no compelling evidence to suggest a maladaptive role of contralesional TI in UE motor recovery in mild-to-moderately impaired stroke subjects. The scattered associations between stronger TI and better levels of paretic UE function suggest a potential supportive role rather than a limiting one. These findings challenge the validity of the interhemispheric competition model in the subacute recovery period, and prompt reconsideration of neuromodulatory strategies that subacutely target contralesional TI.

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AbstractRaised intracranial pressure (ICP) is associated with altered cerebral hemodynamics and cephalic pain. The relationship between the algetic response and cortical neurovascular changes in raised ICP is unclear. This study aimed to evaluate this relationship and determine if lowering ICP (using a glucagon like peptide-1 receptor agonist) could ameliorate the algetic response. We also sought to explore the role of calcitonin gene-related peptide in cephalic pain driven by raised ICP by inhibiting calcitonin gene-related peptide signalling and quantifying changes in the algetic response.In a rat model of raised ICP, created by intracisternal kaolin injection, mechanical thresholds were measured alongside steady-state potential and cerebral blood flow responses to spreading depolarisation. Nuclear magnetic resonance spectroscopy evaluated energetic substrates in animals with raised ICP ex-vivo. Glucagon like peptide-1 receptor agonist exenatide and calcitonin gene-related peptide receptor antagonist olcegepant were injected daily and measurements were repeated.Kaolin increased ICP [median (range) 15.96mmHg (8.97) n = 8] versus controls [6.02mmHg (1.79) n = 6 p = 0.0007]. Animals with raised ICP exhibited reduced mechanical thresholds (mean (SD) hind paw baseline: 5.78g (2.81), day 7: 3.34g (2.22) p < 0.001, periorbital baseline: 6.13g (2.07), day 7: 2.35g (1.91) n = 12 p < 0.001). Depolarisation and repolarisation durations were increased [depolarisation raised ICP: 108.81s (222.12) n = 11, controls: 37.54s (108.38) n = 9 p = 0.038, repolarisation raised ICP: 1824.26s (3499.54) n = 12, controls: 86.96s (140.05) n = 9 p<0.0001]. CBF change was also reduced (85.55% (30.84) n = 9) compared to controls (217.64% (37.70) n = 8 p < 0.0001). Substrates for cellular energetics (ADP, ATP and NAD+) were depleted in rodent brains with raised ICP (p = 0.009, p = 0.018, p = 0.011 respectively).Exenatide significantly lowered ICP (exenatide: 9.74mmHg (6.09) n = 19, vehicle: 18.27mmHg (6.67) n = 16 p = 0.004) and rescued changes in mechanical withdrawal. Exenatide recovered characteristic spreading depolarisation responses (depolarisation duration exenatide: 56.46s (25.10) n = 7, vehicle: 115.98s (58.80) n = 6 p = 0.033) [repolarisation duration exenatide: 177.55s (562.88) n = 7, vehicle: 800.85s (1988.67) n = 6 p = 0.002]. In the setting of raised ICP olcegepant prevented changes in periorbital mechanical thresholds.We conclude that raised ICP disrupted the cortical neurovascular responses, reduced algetic thresholds and depleted crucial energetic substrates. Exenatide reduced ICP, improving algetic thresholds and cortical neurovascular changes. Importantly, olcegepant alleviated the cerebral algesia, suggesting calcitonin gene-related peptide’s role in driving pain responses in elevated ICP.These studies support the rationale that reducing ICP improves cephalic pain in conditions of raised ICP. Furthermore, the data suggests that headache pain, in diseases associated with raised ICP, could be therapeutically ameliorated though blockade of the calcitonin gene-related peptide pathway.

AbstractMalformations of cortical development (MCDs) are a heterogeneous family of congenital brain malformations that originate from disturbed development of the cerebral cortex. MCDs can arise from primary genetic disorders that lead to dysfunction of the molecular processes controlling neuronal proliferation, neuronal migration, cortical folding, or cortical organization. MCDs can also result from secondary, disruptive causes, such as congenital infection or other in utero brain injuries. Sequelae of MCDs can include epilepsy, intellectual disability, and cerebral palsy, among other symptoms, with a high burden of pediatric morbidity. Advances in antenatal genetic testing and imaging have improved the ability to diagnose MCDs, yet limited literature exists to aid clinicians in prognostication of outcomes and perinatal management. These clinical realities can make it challenging for clinicians caring for fetal neurological conditions to counsel families and make recommendations for interdisciplinary care. We aim to review the literature on fetal MCDs and present practice guidelines for clinicians regarding the pre- and postnatal management of MCDs.

AbstractNeuromyelitis optica (NMO) is an acute inflammatory demyelinating disease of the CNS. The presence of astrocyte-targeted AQP4-immunoglobulin G (IgG) in peripheral blood is a major factor in its diagnosis. Previous studies show that AQP4-IgG directly contributes to CNS inflammation, and B cells play a central pathogenic role in NMO. However, where and how B cell response is altered remains controversial. In this study, we comprehensively analyzed with high-parameter flow cytometry the immune cell populations in the CSF samples obtained from first-episode acute-phase NMO patients, and compared to those from patients with acute-phase Multiple Sclerosis (MS) and other neurological diseases (OND). Among ten immune cell populations defined in the analysis, only the frequency of B cells and antibody-secreting cells (ASC) were higher in the CSF of acute-phase NMO compared to OND. Detailed assessments of B cell and ASC subsets in the CSF revealed differences in the dominant subsets between NMO and MS. In NMO, a series of CD21lo B cell subsets ranging from “activated” naïve B, double negative, and switched memory, thus subsets considered as ASC-precursors, were dominant. A majority of these CD21lo B cell subsets expressed CD69 and CXCR3, suggesting their CNS residency. An increase of CD21lo B cell subsets was also observed in the CSF of treatment-refractory NMO patients. Furthermore, two B helper T cell subsets, T peripheral helper type1 and T follicular helper type1 cells, both highly expressing CD69 and CXCR3, were enriched in the CSF of NMO patients, suggesting their interactions with ASC-precursors in the CNS. In vitro culture experiments using blood samples from patients with NMO showed that CD21lo B cells contained AQP4-IgG-producing cells and displayed a high propensity to differentiate into ASCs. We further found that CD21lo B cell subsets in NMO upregulated the expression of C5a receptors, and C5a signals promoted their differentiation into ASCs. ASCs derived from CD21lo B cells expressed high levels of CXCR3 and CD138. The increase in CD21lo B cell subsets significantly correlated with the annual relapse rate. Collectively, our study highly suggests that the mechanism to promote the generation of CD21lo B cells, likely via the extrafollicular pathway, becomes activated during the acute phase of NMO, and the generated CD21lo B cell subsets contribute to the pathogenesis. Targeting CD21lo B cell subsets might be useful for the development of novel therapeutic approaches.

AbstractEpilepsy is recognised as one of the leading targets for precision medicine, following on from the successes in cancer therapy, due to its substantial clinical heterogeneity and divergent therapeutic options. To bring personalised care to the epilepsies, there is a need for appropriate precision biomarkers that can identify disease processes or predict treatment outcomes at the individual patient level. Neuroimaging techniques, including magnetic resonance imaging (MRI), have been transformative for clinical practice, particularly in medically refractory focal epilepsies. Advanced MRI techniques have the potential to bring precision medicine clearly into view for epileptology; however, there are challenges that must be overcome before cutting-edge neuroimaging tools can be used in clinical practice. In this Review article, we communicate our view that implementation of normative modelling frameworks will help to deliver robust quantitative MRI biomarkers for individualized prediction. Here, we provide recommendations for researchers and clinicians alike, from careful research design to clinical applications, that will help to identify diagnostic and predictive imaging biomarkers. Such precision markers will be key to delivering personalised medicine for the epilepsies.

AbstractWhiplash Associated Disorders (WAD) affect 20-50 million individuals globally each year, with up to 50% developing persistent pain. WAD grade II (WADII) is the most common type and is characterised by neck symptoms and musculoskeletal signs without apparent nerve injury on routine diagnostic testing. However, emerging evidence suggests nerve pathology may be present in some people with WADII. This longitudinal cohort study aimed to comprehensively investigate the presence, temporal patterns, and prognostic value of nerve pathology and neuropathic pain in acute WADII.A prospective longitudinal cohort study was conducted with 129 acute participants with WADII (median age 36.0 years, 58% female) and 36 healthy controls (median age 39.0 years, 61% female). Participants with WADII were recruited within four weeks of injury from local emergency departments. Data collection included bedside neurological assessments, quantitative sensory testing (QST), intraepidermal nerve fibre density, and serum neurofilament light chain (NfL) concentrations. Follow-up assessments were conducted 6-months after injury.Signs of neuropathic pain were present in 65% (84/129) acutely and persisted in 32% (21/66) 6-months post-injury. Bedside neurological assessment revealed somatosensory loss of function was present in 54% (70/129) acutely reducing to 25% (17/67) 6-months post-injury. QST demonstrated significantly reduced cold, warm, thermal sensory limen, mechanical, and vibration detection thresholds in acute WADII compared to controls (d>0.47). Acute loss of function in at least one QST parameter was present in 67.6% (85/126) of WADII. At 6-months, participants with WADII showed persistent hypoaesthesia to warm, thermal sensory limen, and mechanical detection thresholds, and decreased mechanical pain and pressure pain sensitivity compared to controls (d>0.44).These functional neurological changes were accompanied by elevated serum neurofilament light chain levels in acute WADII compared to controls (d=-0.52 (95% confidence interval -0.94, -0.10). Intraepidermal nerve fibre densities at the index finger were not significantly different between groups. However, dermal MBP+/PGP+ myelinated nerve bundles at the index finger were reduced 6-months post-injury in WADII compared to controls (d=0.69 (0.26, 1.11). Multivariable linear regression suggested bedside tests for hypoaesthesia at the index finger were prognostic for whiplash-related upper quadrant pain 6-months post-injury (r2=0.13, p=0.02).In conclusion, two-thirds of participants with acute WADII initially exhibited signs of neuropathic pain and nerve pathology. At the 6-month follow-up, neuropathic pain persisted in one-third of participants with WADII, while nerve pathology persisted in two-thirds. These findings challenge the traditional musculoskeletal classification of WADII and underscore the need for targeted neurological assessments and treatment.

Yang et al. propose that psychedelics hold untapped potential for improving stroke recovery through their unique ability to modulate neuroplasticity, reduce neuroinflammation, and enhance cognitive and psychological resilience.

AbstractChildren who experienced moderate perinatal hypoxia are at risk of developing long-lasting subtle cognitive and behavioural deficits, including learning disabilities and emotional problems. Understanding the underlying mechanisms is an essential step for designing targeted therapy. Fast-spiking, parvalbumin-positive (PV) GABAergic interneurons modulate the generation of gamma oscillations, which in turn regulate many cognitive functions including goal-directed attentional processing and cognitive flexibility. Due to their fast-firing rate, PV cell function requires high levels of energy, which may render them highly vulnerable to conditions of metabolic and oxidative stress caused by perinatal hypoxia.Here, we show that adult mice that experienced moderate perinatal hypoxia (MPH) have decreased cortical PV expression levels in addition to specific impairments in social behaviour, recognition memory and cognitive flexibility. We further found that the expression level of the neurotrophin receptor p75NTR, which limits PV cell maturation during the first postnatal weeks, is increased in MPH mice. Genetic deletion of p75NTR in GABAergic neurons expressing the transcription factor Nkx2.1, which include PV cells, protects mice from PV expression loss and the long-term cognitive effects of MPH. Finally, treatment with a p75NTR inhibitor starting after MPH and lasting for a week, prevented PV expression loss and the occurrence of cognitive and cortical activity deficits in adult mice.Altogether our data reveals p75NTR-mediated signaling, as a potential molecular target, for the treatment of the cognitive alterations caused by MPH.

AbstractProteins are involved in multiple biological functions. High-throughput technologies have allowed the measurement of thousands of proteins in population biobanks. In this study, we aimed to identify proteins related to Alzheimer’s disease, Parkinson’s disease, multiple sclerosis and amyotrophic lateral sclerosis by leveraging large-scale genetic and proteomic data.We performed a two-sample cis Mendelian randomization study by selecting instrumental variables for the abundance of >2700 proteins measured by either Olink or SomaScan platforms in plasma from the UK Biobank and the deCODE Health Study. We also used the latest publicly available genome-wide association studies for the neurodegenerative diseases of interest. The potentially causal effect of proteins on neurodegenerative diseases was estimated based on the Wald ratio.We tested 13 377 protein–disease associations, identifying 169 associations that were statistically significant (5% false discovery rate). Evidence of co-localization between plasma protein abundance and disease risk (posterior probability > 0.80) was identified for 61 protein–disease pairs, leading to 50 unique protein–disease associations. Notably, 23 of 50 protein–disease associations corresponded to genetic loci not previously reported by genome-wide association studies. The two-sample Mendelian randomization and co-localization analysis also showed that APOE abundance in plasma was associated with three subcortical volumes (hippocampus, amygdala and nucleus accumbens) and white matter hyper-intensities, whereas PILRA and PILRB abundance in plasma was associated with caudate nucleus volume.Our study provided a comprehensive assessment of the effect of the human proteome that is currently measurable through two different platforms on neurodegenerative diseases. The newly associated proteins indicated the involvement of complement (C1S and C1R), microglia (SIRPA, SIGLEC9 and PRSS8) and lysosomes (CLN5) in Alzheimer’s disease; the interleukin-6 pathway (CTF1) in Parkinson’s disease; lysosomes (TPP1), blood–brain barrier integrity (MFAP2) and astrocytes (TNFSF13) in amyotrophic lateral sclerosis; and blood–brain barrier integrity (VEGFB), oligodendrocytes (PARP1), node of Ranvier and dorsal root ganglion (NCS1, FLRT3 and CDH15) and the innate immune system (CR1, AHSG and WARS) in multiple sclerosis. Our study demonstrates how harnessing large-scale genomic and proteomic data can yield new insights into the role of the plasma proteome in the pathogenesis of neurodegenerative diseases.

AbstractTuberous sclerosis complex (TSC) is an inherited multi-system neurocutaneous disorder where patients often present with neurodevelopmental manifestations such as epilepsy and TSC-associated neuropsychiatric disorder (TAND) that includes autism spectrum disorder (ASD). TSC is caused by inactivating mutations in TSC1 or TSC2 tumor suppressor genes, with encoded proteins hamartin (TSC1) and tuberin (TSC2) forming a functional complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. This has led to treatment with allosteric mTORC1 inhibitor rapamycin analogs (“rapalogs”) for TSC tumors; however, rapalogs are ineffective for treating neurodevelopmental manifestations. mTORC1 signaling controls protein synthesis by regulating formation of the eIF4F complex, with further modulation by MNK1/2 kinases via phosphorylation of the eIF4F subunit eIF4E. While both these pathways modulate translation, comparing their impact on transcriptome-wide mRNA translation, as well as effects of inhibiting these pathways in TSC has not been explored.Employing CRISPR-modified, isogenic neural progenitor cells (NPCs) derived from a female TSC2 patient, we have examined alterations in early neurodevelopmental phenotypes including proliferation and neurite outgrowth, as well as ability of bi-steric mTORC1-specific inhibitor RMC-6272 to rescue these phenotypes. Further, we utilized polysome-profiling to examine transcriptome-wide changes in mRNA translation upon TSC2 loss and tested effects of treatment with RMC-6272 or MNK1/2-specific inhibitor eFT-508.Our results reveal that altered early neurodevelopmental phenotypes can be rescued upon treatment with RMC-6272, but not rapamycin. We also discovered dysregulated mRNA translation in TSC2-Null NPCs, which significantly overlaps with the translatome from TSC1-Null NPCs. Interestingly, numerous non-monogenic ASD-, NDD- and epilepsy-associated genes identified in patients harboring putative loss-of-function mutations, were translationally suppressed in TSC2-Null NPCs. Importantly, translation of these ASD- and NDD-associated genes was reversed upon inhibition of either mTORC1 or MNK1/2 signaling using RMC-6272 or eFT-508, respectively.This study establishes the importance of mTORC1-eIF4F- and MNK-eIF4E-sensitive mRNA translation in TAND, ASD and other neurodevelopmental disorders laying the groundwork for evaluating drugs in clinical development that target these pathways as a treatment strategy for these disorders.

This scientific commentary refers to ‘Distinctive clinical features in biopsy-proven nerve large-arteriole vasculitis and microvasculitis’ by Soontrapa et al. (https://doi.org/10.1093/brain/awae406).

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AbstractGeneral paresis is a rare type of syphilis characterized by progressive cognitive impairment and psychiatric syndromes. It is often misdiagnosed because of its rarity and similarity with other diseases. We aimed to comprehensively investigate the clinical, radiological, pathological, and prognostic features of general paresis, and compare it with other dementias.Between August 2019 and January 2024, patients were recruited from a Memory Clinic Setting of National Center for Neurological Disorders in China. Participants underwent clinical evaluation, laboratory testing, and imaging, and were followed after treatment. Comparative analysis was conducted on clinical features and neuropsychiatric assessments, while brain image features were investigated using linear regression models and SuStaIn models.Seventy-eight patients were included, with 90% being male. The median duration from symptom onset to the first diagnostic visit was 15 months. Sixty-three patients were followed for an average of 1.4 years. Cognitive impairment emerged as the most common symptom, with half of the patients co-existed with motor symptoms. Impairment across all cognitive domains accompanied by positive psychiatric symptoms raised suspicion for general paresis, and distinguishing it from Alzheimer’s disease, frontotemporal dementia, and anti-LGI1 encephalitis-related dementia. Common imaging abnormalities in general paresis included whole brain atrophy and cortical hypointensity. The hippocampal-predominant and hippocampal-sparing atrophy subtypes were identified. Autoimmune responses in general paresis were demonstrated through the detection of autoimmune encephalitis antibodies in 11% of patients. Pathological amyloid changes were observed in 26% of patients, while elevated total tau levels were found in 30%. Seventy percent of patients showed improvement following treatment, with a reduction in the number of symptoms observed across all cases.This study identifies specific clinical syndromes and radiological features of general paresis and refines the understanding of its prognosis. We provide clues to distinguish general paresis from other dementias, facilitating early diagnosis and treatment. The role of novel pathological changes in general paresis needs to be further studied.

AbstractProtease activated receptor 2 (PAR2) is a G-protein coupled receptor expressed in meningeal neurons, fibroblasts and mast cells that may be targeted to treat migraine. MEDI0618, a fully humanized PAR2 monoclonal antibody, engineered to enhance FcRn-dependent recycling and currently in clinical development, was evaluated in human and rodent in vitro assays, in multiple murine in vivo migraine models and in a model of post-traumatic headache.MEDI0618 bound specifically and with high affinity to cells expressing human PAR2 (hPAR2) and prevented matriptase-induced increase in cytosolic calcium. Similarly, MEDI0618 prevented matriptase-induced calcium in primary fibroblasts and microvascular endothelial cells from human dura mater. MEDI0618 had no effect on hPAR1 receptors. Single-cell calcium imaging of acutely dissociated mouse trigeminal ganglion neurons confirmed expression and functionality of mouse PAR2. Studies in vivo used evoked cutaneous allodynia as a surrogate of headache-like pain and, in some experiments, rearing as a measure of non-evoked headache pain. MEDI0618 was administered subcutaneously to C57BL6/J female mice prior to induction of migraine-like pain with (i) systemic nitroglycerin or compound 48/80 (mast cell degranulator); or (ii) with supradural compound 48/80 or an inflammatory mediator (IM) cocktail. To assess possible efficacy against CGRP receptor (CGRP-R)-independent pain, MEDI0618 was also evaluated in the IM model in animals pretreated with systemic olcegepant (CGRP-R antagonist). Migraine-like pain was also induced by inhalational umbellulone, a TRPA1 agonist, in animals primed with restraint stress in the presence or absence of MEDI0618 as well as in a model of post-traumatic headache pain induced by a mild traumatic brain injury.MEDI0618 prevented cutaneous allodynia elicited by systemic nitroglycerin, compound 48/80 and from supradural compound 48/80 and IM. Systemic olcegepant completely blocked periorbital cutaneous allodynia induced by supradural CGRP but failed to reduce IM-induced cutaneous allodynia. In contrast, MEDI0618 fully prevented IM-induced cutaneous allodynia, regardless of pretreatment with olcegepant. Umbellulone elicited cutaneous allodynia only in restraint stress-primed animals, which was prevented by MEDI0618. MEDI0618 prevented the decrease in rearing behaviour elicited by compound 48/80. However, MEDI0618 did not prevent mild traumatic brain injury-related post-traumatic headache measures.These data indicate that MEDI0618 is a potent and selective inhibitor of PAR2 that is effective in human and rodent in vitro cell systems. Further, blockade of PAR2 with MEDI0618 was effective in all preclinical migraine models studied but not in a model of post-traumatic headache. MEDI0618 may represent a novel therapy for migraine prevention with activity against CGRP-dependent and independent attacks.

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AbstractNeuroinflammation is a feature of many neurodegenerative diseases, and is quantified in vivo by PET imaging with radioligands for the translocator protein (TSPO, e.g. [11C]-PK11195). TSPO radioligand binding correlates with clinical severity and predicts clinical progression. However, the cellular substrate of altered TSPO binding is controversial and requires neuropathological validation.We used progressive supranuclear palsy (PSP) as a demonstrator condition, to test the hypothesis that [11C]-PK11195 PET reflects microglial changes. We included people with PSP-Richardson’s syndrome who had undergone [11C]-PK11195 PET in life (n=8). In post-mortem brain tissue from the same participants, we characterised cell-type specific TSPO expression and quantified microgliosis in eight cortical and eleven subcortical regions.Double-immunofluorescence labelling for TSPO and cell markers showed TSPO expression in microglia, astrocytes, and endothelial cells. Microglial (and not astrocytic) TSPO levels were higher in donors with PSP compared to controls (n=3), and correlated with changes in microglial density. There was a significant positive correlation between regional [11C]-PK11195 binding potential ante-mortem and the density of post-mortem CD68+ phagocytic microglia, as well as microglial TSPO levels.We conclude that in vivo disease-related changes in [11C]-PK11195 binding is largely driven by microglia and can be interpreted as a biomarker of microglia-mediated neuroinflammation in tauopathies.

AbstractWhile neuropathological and genetic studies have established the crucial involvement of TDP-43 proteinopathy in the pathogenesis of ALS (Amyotrophic Lateral Sclerosis), FTD (Frontotemporal Dementia) and related neurodegenerative disorders, multiple studies have described the presence of TDP-43 inclusions in muscular disorders, including inclusion body myositis but also other related rimmed vacuole myopathies. In addition, TDP-43 has been reported to be essential in normal muscle physiology as it is implicated in the formation of so-called amyloid-like myogranules during normal muscle regeneration after injury. However, genetic evidence supporting a primary role for TDP-43 proteinopathy in muscle disease has been missing. In the present review we highlight recent landmark discoveries linking novel pathogenic TDP-43 variants [p.(W385IfsX10) and p.(G376V)] within the prion-like domain with unusual aggregation-propensity and muscle rather than neuronal pathology. We discuss these studies in the context of known TDP-43-related pathways in ALS/FTD pathogenesis and show how they challenge some widely accepted views such as ALS as a pure neurogenic presynaptic neuromuscular disease and the direct correlation between TDP-43 aggregation-propensity and neurotoxicity. Finally, we discuss TDP-43 as part of a growing list of RNA-binding proteins including hnRNPA2B1 and hnRNPA1 as genetic causes of myopathies and relate this to the idea of ‘multisystem proteinopathy’.

AbstractFunctional neuroimaging has provided several new tools for improving both the diagnosis and prognosis in patients with DoC. These tools are now being used to detect residual and covert awareness in behaviourally non-responsive patients with an acquired severe brain injury and predict which patients are likely to recover. Despite endorsement of advanced imaging by multiple clinical bodies, widespread implementation of imaging techniques such as functional MRI (fMRI), electroencephalography (EEG), and positron emission tomography (PET) in both acute and prolonged disorders of consciousness patients has been hindered by perceived costs, technological barriers, and lack of expertise needed to acquire, interpret, and implement these methods. In this review we provide a comprehensive overview of neuroimaging in DoC, the different technical approaches employed (i.e. fMRI, EEG, PET), the imaging paradigms used (active, passive, resting state) and the types of inferences that have been made about residual cortical function based on those paradigms (e.g., perception, awareness, communication). Next, we outline how these barriers might be overcome, discuss which select patients stand to benefit the most from these neuroimaging techniques, and consider when during their clinical trajectory imaging tests are likely to be most useful. Moreover, we make recommendations that will help clinicians decide which advanced imaging technologies and protocols are likely to be most appropriate in any particular clinical case. Finally, we describe how these techniques can be implemented in routine clinical care to augment current clinical tools and outline future directions for the field as a whole.

AbstractMutations in myelin protein zero (MPZ) are generally associated with Charcot-Marie-Tooth type 1B (CMT1B) disease, one of the most common forms of demyelinating neuropathy. Pathogenesis of some MPZ mutants, such as S63del and R98C, involves the misfolding and retention of MPZ in the endoplasmic reticulum (ER) of myelinating Schwann cells. To cope with proteotoxic ER-stress, Schwann cells mount an unfolded protein response (UPR) characterized by activation of the PERK, ATF6 and IRE1α/XBP1 pathways. Previous results showed that targeting the PERK UPR pathway mitigates neuropathy in mouse models of CMT1B; however, the contributions of other UPR pathways in disease pathogenesis remains poorly understood.Here, we probe the importance of the IRE1α/XBP1 signalling during normal myelination and in CMT1B. In response to ER stress, IRE1α is activated to stimulate the non-canonical splicing of Xbp1 mRNA to generate spliced Xbp1 (Xbp1s). This results in the increased expression of the adaptive transcription factor XBP1s, which regulates the expression of genes involved in diverse pathways including ER proteostasis. We generated mouse models where Xbp1 is deleted specifically in Schwann cells, preventing XBP1s activation in these cells. We observed that Xbp1 is dispensable for normal developmental myelination, myelin maintenance and remyelination after injury. However, Xbp1 deletion dramatically worsens the hypomyelination and the electrophysiological and locomotor parameters observed in young and adult CMT1B neuropathic animals. RNAseq analysis suggested that XBP1s exerts its adaptive function in CMT1B mouse models in large part via the induction of ER proteostasis genes. Accordingly, the exacerbation of the neuropathy in Xbp1 deficient mice was accompanied by upregulation of ER-stress pathways and of IRE1-mediated RIDD signaling in Schwann cells, suggesting that the activation of XBP1s via IRE1 plays a critical role in limiting mutant protein toxicity and that this toxicity cannot be compensated by other stress responses. Schwann cell specific overexpression of XBP1s partially re-established Schwann cell proteostasis and attenuated CMT1B severity in both the S63del and R98C mouse models. In addition, the selective, pharmacologic activation of IRE1α/XBP1 signaling ameliorated myelination in S63del dorsal root ganglia explants.Collectively, these data show that XBP1 has an essential adaptive role in different models of proteotoxic CMT1B neuropathy and suggest that activation of the IRE1α/XBP1 pathway may represent a therapeutic avenue in CMT1B and possibly for other neuropathies characterized by UPR activation.

AbstractSpinal muscular atrophy (SMA) is a neurodegenerative disease characterized by a varying degree of severity that correlates with the reduction of SMN protein levels. Motor neuron degeneration and skeletal muscle atrophy are hallmarks of SMA, but it is unknown whether other mechanisms contribute to the spectrum of clinical phenotypes.Here, through a combination of physiological and morphological studies in mouse models and SMA patients, we identify dysfunction and loss of proprioceptive sensory synapses as key signatures of SMA pathology. We demonstrate that Type 3 SMA patients exhibit impaired proprioception, and their proprioceptive synapses are dysfunctional as measured by the neurophysiological test of the Hoffmann reflex (H-reflex). We further show moderate loss of spinal motor neurons along with reduced excitatory afferent synapses and altered potassium channel expression in motor neurons from Type 1 SMA patients. These are conserved pathogenic events found in both severely affected patients and mouse models. Lastly, we report that improved motor function and fatigability in ambulatory Type 3 SMA patients and mouse models treated with SMN-inducing drugs correlate with increased function of sensory-motor circuits that can be accurately captured by the H-reflex assay.Thus, sensory synaptic dysfunction is a clinically relevant event in SMA, and the H-reflex is a suitable assay to monitor disease progression and treatment efficacy of motor circuit pathology.

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AbstractElevated beta (β; 13-30 Hz) synchronization within the subthalamic nucleus (STN) characterizes bradykinesia in Parkinson’s disease (PD). β oscillations may serve as biomarkers for off-period motor symptoms and control signals for adaptive, closed-loop deep brain stimulation (DBS) in PD. However, their relation to striatal dopaminergic denervation and PD progression remains uncertain. Research on β oscillations is limited to advanced PD stages undergoing DBS, prohibiting insights into early-stage progression and compensatory mechanisms. We therefore investigated β dynamics, correlation with motor performance, and nigrostriatal neurodegeneration in a progressive PD rat model overexpressing AAV1/2-A53T α-synuclein, mimicking PD pathology.Over eight weeks, we longitudinally conducted behavioral assessments using the cylinder test and recorded local field potentials (LFP) from the STN and motor cortex (MCx) in the AAV-A53T-αSyn PD rat model.Increased β power and burst parameters accompanied early motor deficits in the AAV-A53T-αSyn PD rat model. Changes were observed in the STN and MCx versus empty vector controls; alterations intensified with pathology progression. Increased high β power and burst parameters (e.g. long burst probability in the STN but not MCx) were associated with motor impairment and nigrostriatal dopaminergic neurodegeneration. Multivariate analyses from these rat-derived data demonstrated that combined β parameters in the cortico-subthalamic pathway and striatal dopaminergic fiber density predicted motor performance and neurodegeneration. Additional multivariate analyses confirmed the translational relevance of the A53T PD model, linking β activity and dopamine uptake to motor impairment (UPDRS III Med-OFF) in human PD patients. Our data support the pathophysiological significance of β oscillations as a progression marker of PD for motor symptoms and neurodegeneration. Our predictive models carry translational relevance, with the prospect of monitoring disease progression and neuroprotective outcomes in PD based on LFP recordings.

Determining the validity and reliability of a test is crucial when the results inform clinical decision-making. Voets et al. highlight priority areas where progress is needed to resolve long-standing controversies surrounding clinical applications of functional MRI in neurosurgery.

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Dynamic processes involving biomolecules are essential for the function of the cell. Here, we introduce an integrative method for computing models of these processes based on multiple heterogeneous sources of information, including time-resolved experimental data and physical models of dynamic processes. First, for each time point, a set of coarse models of compositional and structural heterogeneity is computed (heterogeneity models). Second, for each heterogeneity model, a set of static integrative structure models is computed (a snapshot model). Finally, these snapshot models are selected and connected into a series of trajectories that optimize the likelihood of both the snapshot models and transitions between them (a trajectory model). The method is demonstrated by application to the assembly process of the human nuclear pore complex in the context of the reforming nuclear envelope during mitotic cell division, based on live-cell correlated electron tomography, bulk fluorescence correlation spectroscopy–calibrated quantitative live imaging, and a structural model of the fully assembled nuclear pore complex. Modeling of the assembly process improves the model precision over static integrative structure modeling alone. The method is applicable to a wide range of time-dependent systems in cell biology and is available to the broader scientific community through an implementation in the open sourceIntegrative Modeling Platform (IMP)software.

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The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Microbial competition for these scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism that can structure uptake of limiting nutrients and facilitate coexistence of diverse microbes in open ocean ecosystems.

Active turbulence, or chaotic self-organized collective motion, is often observed in concentrated suspensions of motile bacteria and other systems of self-propelled interacting agents. To date, there is no fundamental understanding of how geometrical confinement orchestrates active turbulence and alters its physical properties. Here, by combining large-scale experiments, computer modeling, and analytical theory, we have identified a generic sequence of transitions occurring in bacterial suspensions confined in cylindrical wells of varying radii. With increasing the well’s radius, we observed that persistent vortex motion gives way to periodic vortex reversals, four-vortex pulsations, and then well-developed active turbulence. Using computational modeling and analytical theory, we have shown that vortex reversal results from the nonlinear interaction of the first three azimuthal modes that become unstable with the radius increase. The analytical results account for our key experimental findings. To further validate our approach, we reconstructed equations of motion from experimental data. Our findings shed light on the universal properties of confined bacterial active matter and can be applied to various biological and synthetic active systems.

At the end of their growth phase,Drosophilalarvae remodel their bodies, glue themselves to a substrate, and harden their cuticle in preparation for metamorphosis. This process—termed pupariation—is triggered by a surge in the hormone ecdysone. Substrate attachment is achieved by a pupariation subprogram called glue expulsion and spreading behavior (GSB). An epidermis-to-CNS Dilp8-Lgr3 relaxin signaling event that occurs downstream of ecdysone is critical for unlocking progression of the pupariation motor program toward GSB, but the factors and circuits acting downstream of Lgr3 signaling remain unknown. Here, using cell-type-specific RNA interference and behavioral monitoring, we identify Myoinhibiting peptide (Mip) as a neuromodulator of multiple GSB action components, such as tetanic contraction, peristaltic contraction alternation, and head-waving. Mip is required in a pair of brain descending neurons, which act temporally downstream of Dilp8-Lgr3 signaling. Mip modulates GSB via ventral nerve cord neurons expressing its conserved receptor, sex peptide receptor (SPR). Silencing of Mip descending neurons by hyperpolarization completely abrogates GSB, while their optogenetic activation at a restricted competence time window triggers GSB-like behavior. Hence, Mip descending neurons have at least two functions: to act as GSB command neurons and to secrete Mip to modulate GSB action components. Our results provide insight into conserved aspects of Mip-SPR signaling in animals, reveal the complexity of GSB control, and contribute to the understanding of how multistep innate behaviors are coordinated in time and with other developmental processes through command neurons and neuropeptidergic signaling.

Deforestation frequently accompanies poverty, yet various antipoverty programs in many countries have exhibited mixed results in addressing deforestation. Poverty Alleviation Resettlement (PAR) stands out as one of the few government-led resettlement programs designed to alleviate poverty, offering comprehensive follow-up support for quality of life and employment after relocation. Our study uncovered empirical evidence of the PAR program’s impact on forest quality. Through a multiperiod difference-in-differences analysis of remote sensing and household survey data, we found that the PAR program significantly curbed deforestation in the participating counties and reduced forest-clearing activities among the resettled households, even those relocating to rural villages. Mechanism analysis revealed that the program discouraged deforestation by enhancing market accessibility, fostering nonfarm employment opportunities, and elevating income levels. The study underscores that altering livelihood strategies and lifestyles is essential for resettlement programs to effectively mitigate ecological degradation.

We study the driven-dissipative Bose-Hubbard model with an all-to-all hopping term in the system Hamiltonian, while subject to incoherent pumping and decay from the environment. This system is naturally probed in several recent experiments on excitons in WS2/WSe2moiré systems, as well as quantum simulators. By positing a particular form of coupling to the environment, we derive the Lindblad jump operators and show that, in certain limits, the system admits a closed-form expression for the steady-state density matrix. Away from the exactly solvable regions, the steady state can be obtained numerically for 100s to 1,000s of sites. We study the nonequilibrium phase diagram and phase transitions, which qualitatively matches the equilibrium phase diagram, agreeing with the intuition that increasing the intensity of the light is equivalent to changing the bosonic chemical potential. However, the steady states are far from thermal states, and the nature of the phase transitions is changed.

Dopamine (DA) signals to the striatum play critical roles in shaping and sustaining stimulus-reward associations. In primates, however, the dynamics of the DA signals remain unknown since conventional methods are not necessarily appropriate in terms of the spatiotemporal resolution or chemical specificity sufficient for detecting the DA signals. In our study, fiber photometry with a fluorescent DA sensor was employed to identify reward-related DA transients in the monkey striatum. This technique, which directly monitors local DA release, reveals a reward prediction error signal in the anterior putamen originating from midbrain DA neurons. Further, DA transients in the head of the caudate nucleus exhibit a value-based response to reward-predicting stimuli. These signals have been found to arise from two separate groups of DA neurons in the substantia nigra pars compacta. The present results demonstrate that fluorescence DA monitoring is applicable to detect DA signals in the primate striatum for investigating their roles.

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Neuropathic pain is a debilitating chronic condition mainly caused by peripheral nerve injury. However, the cellular and molecular mechanisms underlying this condition remain unclear. Transient receptor potential canonical 3 (TRPC3), a TRP channel that is activated by downstream of the Gq-phospholipase C (PLC) axis, is expressed in the somatosensory system. Therefore, the present study investigated its pathophysiological role in neuropathic pain following peripheral nerve injury. Here, partial sciatic nerve ligation (pSNL) elicited mechanical and thermal hypersensitivity in wild-type mice, which was suppressed in TRPC3-KO mice. In situ hybridization revealed that TRPC3 is predominantly expressed in neurons in the spinal dorsal horn. Furthermore, spinal dorsal horn neuron-specific downregulation using miRNA attenuated pSNL-induced mechanical hypersensitivity. Spinal TRPC3 activation elicited acute mechanical hypersensitivity. Moreover, its genetic ablation reduced the mechanical hypersensitivity caused by spinal NK1R or PLC activation. These findings demonstrate that TRPC3 in spinal dorsal horn neurons facilitates the development of neuropathic pain. Therefore, TRPC3 may be a promising therapeutic target for neuropathic pain caused by peripheral nerve injury.

Mixed-species plantations are increasingly recognized for their potential to maintain forest biodiversity and soil health; however, a comprehensive assessment of their global effectiveness is lacking. To fill this knowledge gap, we conducted a meta-analysis of 7,045 paired observations between mixed-species and monoculture plantations, derived from 311 studies across diverse forest ecosystems worldwide. Our results show that mixed-species plantations significantly increased understory plant biomass, cover, and species richness by 32.6%, 55.4%, and 32.2%, respectively, compared to monocultures. Furthermore, the Shannon and Pielou diversity indices increased by 28.2% and 8.6%, respectively, and the Simpson index increased by 9.6%. When understory shrub and herbaceous species were considered separately, species mixing had significantly positive effects on shrub diversity but had no effect on herbaceous diversity. Moreover, mixed-species plantations markedly improved soil physical and chemical properties compared to monocultures. These improvements include increases in soil nutrient content (9.6 to 17.8%) and nutrient availability (14.7 to 33.5%), soil microbial biomass (17.2 to 28.8%), and soil carbon sequestration (7.2 to 19.9%). These enhancements were particularly pronounced in plantations that included legumes. Our findings reveal that the benefits of species mixing are influenced by climatic conditions, geographic location, and stand age, with the most substantial effects observed in temperate regions and mature stands. This study underscores the critical role of mixed-species plantations in promoting sustainable forest management and mitigating the ecological limitations of monocultures.

We study how self-organization in systems showing complex spatiotemporal dynamics can increase ecosystem resilience. We consider a general simple model that includes positive feedback as well as negative feedback mediated by an inhibitor. We apply this model toPosidonia oceanicameadows, where positive and negative feedbacks are well documented, and there is empirical evidence of the role of sulfide accumulation, toxic for the plant, in driving complex spatiotemporal dynamics. We describe a progressive transition from homogeneous meadows to extinction through dynamical regimes that allow the ecosystem to avoid the typical ecological tipping points of homogeneous vegetation covers. A predictable sequence of distinct dynamical regimes is observed as mortality is continuously increased: turbulent regimes, formation of spirals and wave trains, and isolated traveling pulses or expanding rings, the latter being a harbinger of ecosystem collapse, however far beyond the tipping point of the homogeneous cover. The model used in this paper is general, and the results can be applied to other plant–soil spatially extended systems, regardless of the mechanisms behind negative and positive feedbacks.

The importance of macrophages in kidney diseases has been well established; however, the mechanisms underlying the infiltration of macrophages into injured kidneys are not well understood. RGMb is a member of the repulsive guidance molecule (RGM) family. RGMb can be expressed on the cell surface but a large portion of RGMb is localized intracellularly. Among various immune cell types, macrophages express the highest levels of RGMb, but the biological functions of RGMb in macrophages remain largely unknown. We find that RGMb promoted macrophage migration in vitro and that in vivo, RGMb enhanced infiltration of macrophages into injured kidneys and aggravated kidney inflammation and injury in mice. Mechanistically, RGMb bound to TAB1 inside the cell and facilitated the interaction between TRAF6 ubiquitin ligase and TAB1, thereby promoting TRAF6-mediated K63-linked polyubiquitination and phosphorylation of TAK1, followed by increased αTAT1 phosphorylation and α-tubulin acetylation. The resulting changes in the cytoskeleton promoted macrophage migration in vitro and in vivo. Deletion of Rgmb in macrophages markedly reduced TAK1 phosphorylation, αTAT1 phosphorylation, and α-tubulin acetylation and attenuated macrophage infiltration, renal inflammation, tubular injury, and interstitial fibrosis during kidney injury. Our results suggest that macrophage RGMb promotes kidney disease by increasing macrophage infiltration via the TRAF6-TAB1-TAK1/αTAT1/α-tubulin cascade.

As infants grow, they develop greater attentional control during interactions with others, shifting from patterns of attention primarily driven by caregivers (exogenous) to those that are also self-directed (endogenous). The ability to endogenously control attention during infancy is thought to reflect ongoing brain development and is influenced by patterns of joint attention between infant and caregiver. However, whether measures of infant attentional control and caregiver behavior during infant–caregiver interactions relate to patterns of infant brain activity is unknown and key for informing developmental models of attentional control. Using data from 43 infant–caregiver dyads, we quantified patterns of visual attention with dyadic, head-mounted eye tracking during infant–caregiver play and associated them with the duration of infant EEG microstate D/4 measured during rest. Importantly, microstate D/4 is a scalp potential topography thought to reflect the organization and function of attention-related brain networks. We found that microstate D/4 associated positively with infant-led joint attention rate but did not associate with caregiver-led joint attention rate, suggesting that infant-led coordination of joint attention during play may be critical for the neurobiological development of attentional control, or vice versa. Further, we found that microstate D/4 associated negatively with infant attention shift rate and positively with infant sustained attention duration, suggesting that increased stability of microstate D/4 may reflect maturation of attentional control and its underlying neural substrates. Together, our findings provide insights into how infant attentional control abilities and infant–caregiver visual behavior during play are associated with the spatial and temporal dynamics of infant brain activity.

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Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial inflammation, pannus formation, and progressive joint destruction. The inflammatory milieu in RA drives endothelial cell activation and upregulation of adhesion molecules, thus facilitating leukocyte infiltration into the synovium. Reelin, a circulating glycoprotein previously implicated in endothelial activation and leukocyte recruitment in diseases such as atherosclerosis and multiple sclerosis, has emerged as a potential upstream regulator of these processes. However, its role in RA pathogenesis remains poorly understood. Here, we demonstrate that Reelin levels are markedly elevated in the plasma of both RA patients and mouse models of arthritis, with higher concentrations correlating with greater disease severity. Genetic deletion of the Reelin receptor Apoer2 conferred significant protection against serum transfer arthritis (STA), underscoring the relevance of this pathway in disease progression. Furthermore, therapeutic inhibition of Reelin using the CR-50 antibody yielded robust anti-inflammatory effects in multiple preclinical arthritis models, including STA, K/BxN, and collagen-induced arthritis. Notably, CR-50 treatment not only reduced leukocyte infiltration and synovial inflammation but also mitigated pannus formation. Importantly, these benefits were achieved without the gastrointestinal side effects commonly associated with nonsteroidal anti-inflammatory drugs like diclofenac. Our findings position Reelin as a proinflammatory endothelial biomarker and therapeutic target in RA. By modulating endothelial activation and leukocyte recruitment, anti-Reelin strategies offer an alternative approach to attenuate synovial inflammation and joint damage. These results provide a compelling rationale for further exploration of Reelin-targeted therapies as alternatives to conventional immunosuppressive treatments in RA and other chronic inflammatory diseases.

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Chronic infections with hepatitis E virus (HEV), especially those of genotype 3 (G3), frequently lead to liver fibrosis and cirrhosis in patients. However, the causation and mechanism of liver fibrosis triggered by chronic HEV infection remain poorly understood. Here, we found that the viral multiple-domain replicase (ORF1) undergoes unique ubiquitin–proteasomal processing leading to formation of theHEV-DerivedSMADActivator (HDSA), a viral polypeptide lacking putative helicase and RNA polymerase domains. The HDSA is stable, non-HSP90-bound, localizes to the nucleus, and is abundant in G3 HEV-infected hepatocytes of various origins. Markedly, the HDSA in hepatocytes potentiates the fibrogenic TGF-β/SMAD pathway by forming compact complexes with SMAD3 to facilitate its promoter binding and coactivator recruitment, leading to significant fibrosis in HEV-susceptible gerbils. Virus infection–induced liver fibrosis in HEV-susceptible gerbils could be prevented by mutating the residues P989C, A990C, and A991C (PAA-3C) within ORF1, which are required for proteasomal processing. Thus, we have identified a viral protein derived from host proteasomal processing, defined its notable role in liver fibrosis and highlighted the nature of an unanticipated host–HEV interaction that facilitates hepatitis E pathogenesis.

CRISPR-Cas9 systems have revolutionized biotechnology, creating diverse new opportunities for biomedical research and therapeutic genome and epigenome editing. Despite the abundance of bacterial CRISPR-Cas9 systems, relatively few are effective in human cells, limiting the overall potential of CRISPR technology. To expand the CRISPR-Cas toolbox, we characterized a set of type II CRISPR-Cas9 systems from select bacterial genera and species encoding diverse Cas9s. Four systems demonstrated robust and specific gene repression in human cells when used as nuclease-null dCas9s fused with a KRAB domain and were also highly active nucleases in human cells. These systems have distinct protospacer adjacent motifs (PAMs), including AT-rich motifs and sgRNA features orthogonal to the commonly usedStaphylococcus aureusandStreptococcus pyogenesCas9s. Additionally, we assessed gene activation when fused with the p300 catalytic domain. Notably,S. uberisCas9 performed competitively against benchmarks with promising repression, activation, nuclease, and base editing activity. This study expands the CRISPR-Cas9 repertoire, enabling effective genome and epigenome editing for diverse applications.

Nonlinear plasma physics problems are usually simulated through comprehensive modeling of phase space. The extreme computational cost of such simulations has motivated the development of multi-moment fluid models. However, a major challenge has been finding a suitable fluid closure for these fluid models. Recent developments in physics-informed machine learning have led to a renewed interest in constructing accurate fluid closure terms. In this study, we take an approach that integrates kinetic physics from the first-principles Vlasov simulations into a fluid model (through the heat flux closure term) using the Fourier neural operator—a neural network architecture. Without resolving the phase space dynamics, this new fluid model is capable of capturing the nonlinear evolution of the Landau damping process that exactly matches the Vlasov simulation results. This machine learning–assisted new approach provides a computationally affordable framework that surpasses previous fluid models in accurately modeling the kinetic evolution of complex plasma systems.

Resting brain activity, in the absence of explicit tasks, appears as distributed spatiotemporal patterns that reflect structural connectivity and correlate with behavioral traits. However, its role in shaping behavior remains unclear. Recent evidence shows that resting-state spatial patterns not only align with task-evoked topographies but also encode distinct visual (e.g., lines, contours, faces, places) and motor (e.g., hand postures) features, suggesting mechanisms for long-term storage and predictive coding. While prior research focused on static, time-averaged task activations, we examine whether dynamic, time-varying motor states seen during active hand movements are also present at rest. Three distinct motor activation states, engaging the motor cortex alongside sensory and association areas, were identified. These states appeared both at rest and during task execution but underwent temporal reorganization from rest to task. Thus, resting-state dynamics serve as strong spatiotemporal priors for task-based activation. Critically, resting-state patterns more closely resembled those associated with frequent ecological hand movements than with an unfamiliar movement, indicating a structured repertoire of movement patterns that is replayed at rest and reorganized during action. This suggests that spontaneous neural activity provides priors for future movements and contributes to long-term memory storage, reinforcing the functional interplay between resting and task-driven brain activity.

In emulsions of multicomponent fluids, the dispersed phase forms tiny droplets in the continuous phase. In situ control and manipulation to achieve diversity in emulsion droplets for emerging applications is challenging. In a liquid crystal-based emulsion, the surface anchoring of the molecules at the isotropic fluid-liquid crystal interface introduces elastic distortions that result in anisotropic interparticle interactions, similar to electrostatic interactions between multipoles, which also lends a naming analogy as elastic dipoles, quadrupoles, and higher. However, controlling the anchoring condition at the interface at will is rarely achieved. Here, we present an emulsion system in which silicone oil droplets in a nematic liquid crystal spontaneously induce conic surface anchoring, forming elastic hexadecapoles without any surfactant. The conic degenerate surface anchoring shows continuous reversible anchoring transition to tangential and homeotropic below and above the ambient temperature, respectively. We introduce a physical design principle and in situ control to achieve three-phase compound droplets with diverse morphologies and topologies by fusing elastic hexadecapoles of oil droplets with elastic dipoles of glycerol droplets. The surrounding director field and the resulting defect structure of the compound droplets are analyzed by numerical simulations. Our approach to forming compound droplets will allow the on-demand design of building blocks for engineered emulsions for reconfigurable composite materials.

N6-methyladnosine (m6A) modification is present in both positive- and negative-strand RNA of influenza A virus (IAV) and affects the replication and pathogenicity of IAV. However, little is known about the regulatory mechanism of m6A in IAV RNA. In the present study, we identified the m6A methylation of the viral RNA of different IAV subtypes and confirmed that m6A modification promotes the polymerase activity and replication of IAV. By mutating m6A motifs on the multiple viral RNAs (vRNAs) of IAV, we revealed that m6A deficiency in vRNA suppresses the expression of viral genes and the replication of the virus in vitro. In addition, m6A deficiency in vRNA reduced the pathogenicity of IAV in a mouse model. Mechanistically, m6A deficiency in vRNA suppresses the assembly of the viral ribonucleoprotein (vRNP) complex by impairing the interaction between vRNA and vRNP proteins in an m6A methyltransferase-dependent manner, but not the m6A reader proteins. Together, our findings reveal an important role for m6A on viral RNAs in facilitating the activity of the polymerase complex and the replication and pathogenicity of IAV, which provides insights for the development of novel anti-influenza strategies.

Sinorhizobium melilotiis a soil bacterium that establishes a nitrogen-fixing symbiosis within root nodules of legumes. In this symbiosis,S. melilotiundergoes a drastic cellular change leading to a terminally differentiated form, called bacteroid, characterized by genome endoreduplication, increased cell size, and high membrane permeability. Bacterial cell cycle (mis)regulation is at the heart of this differentiation process. In free-living cells, the master regulator CtrA ensures the progression of cell cycle by activating cell division (controlled by FtsZ) and inhibiting DNA replication, while on the other hand the so far poorly unknown downregulation of CtrA and FtsZ is essential for bacteroid differentiation. Here, we combine cell biology, biochemistry, and bacterial genetics to understand the functions of FcrX, a factor that controls both CtrA and FtsZ in free-living growth and in symbiosis. Depletion of the essential genefcrXled to abnormally high levels of FtsZ and CtrA and minicell formation. Using multiple complementary techniques, we showed that FcrX may interact with FtsZ and CtrA. Moreover,fcrXtranscription is directly controlled by CtrA itself and the FcrX protein displays a cell cycle-dependent pattern. We showed further that FcrX also binds the degradosome complex ClpXP and its adaptors CpdR1 and RcdA, and that CtrA degradation efficiency depends on FcrX. We further showed that, despite weak homology with FliJ-like proteins, only FcrX proteins from closely related species are able to complementS. meliloti fcrXfunction. Finally, deregulation of FcrX showed abnormal symbiotic behaviors in plants suggesting a putative role of this factor during bacteroid differentiation.

Muscle contraction is driven by myosin motors from the thick filaments pulling on the actin-containing thin filaments of the sarcomere, and it is regulated by structural changes in both filaments. Thin filaments are activated by an increase in intracellular calcium concentration [Ca2+]iand by myosin binding to actin. Thick filaments are activated by direct sensing of the filament load. However, these mechanisms cannot explain muscle relaxation when [Ca2+]idecreases at high load and myosin motors are attached to actin. There is, therefore, a fundamental gap in our understanding of muscle relaxation, despite its importance for muscle function in vivo, for example, for rapid eye movements or, on slower timescales, for the efficient control of posture. Here, we used time-resolved small-angle X-ray diffraction (SAXD) to determine how muscle thin and thick filaments switch OFF in extensor digitorum longus (EDL) muscles of the mouse in response to decreases in either [Ca2+]ior muscle load and to describe the distribution of muscle sarcomere lengths (SLs) during relaxation. We show that reducing load at high [Ca2+]iis more effective in switching OFF both the thick and thin filaments than reducing [Ca2+]iat high load in normal relaxation. In the latter case, the thick filaments initially remain fully ON, although the number of myosin motors bound to actin decreases and the force per attached motor increases. That initial slow phase of relaxation is abruptly terminated by yielding of one population of sarcomeres, triggering a redistribution of SLs that leads to the rapid completion of mechanical relaxation.

Central emotion theories assume that during threatening and dangerous events the human face signals a prototypical, distinct, and universally recognized expression of fear which can be accurately decoded by conspecific perceivers. Due to the importance of fear expressions, an unusually large body of research has been dedicated to exploring their evolutionary origins, neurobiological mechanisms, and clinical significance. However, these studies typically utilize highly recognizable posed actor portrayals presumed to closely resemble the diagnostic physical appearance of real-life fearful faces. Here, we challenge this diagnosticity assumption. Following context-dependent frameworks (Barrett, 2017), we hypothesized that extrafacial context (e.g., situational information, body posture, etc.) plays a far greater role in fear communication than the signal of the isolated face. In 12 preregistered experiments (N = 4,180), we examined the perception of authentic, real-life videos documenting a diverse range of intense fear-inducing situations (e.g., height jumping, physical attacks, exposure to phobia triggers). Participants viewed the face alone, the context with no face, or the full video while various response methods of emotion perception were tested (forced choice, open-ended, multiple emotion scales, valence-arousal ratings). Across experiments, videos of the faces alone failed to communicate fear in a reliable manner. In sharp contrast, context with no faces, and faces with context were clearly and robustly perceived as fearful, with medium to large effect sizes. These findings suggest that despite the undisputed importance of perceiving fear reactions, facial expressions alone bear minimal diagnostic value, while context plays a critical role in real-life fear perception.

Autocratic governments around the world use clandestine propaganda campaigns to influence the media. We document a decade-long trend in China toward the planting of government-authored articles in party and commercial newspapers. To examine this phenomenon, we develop an approach to identifying scripted propaganda—the coerced reprinting of lightly adapted government-authored articles in newspapers—that leverages the footprints left by the government when making media interventions. We show that in China, scripted propaganda is a daily phenomenon—on 90% of days from 2012 to 2022, the vast majority of party newspapers include at least some scripted propaganda at the direction of a central directive. On particular sensitive days, the amount of scripted propaganda can spike to 30% of the articles appearing in major newspapers. We show that scripted propaganda has strengthened under President Xi Jinping. In the last decade, the front page of party newspapers has evolved from 5% scripted articles to approximately 20% scripted. This government-authored content throughout the paper is increasingly homogeneous—fewer and fewer adaptations are done by individual newspapers. In contrast to popular speculation, we show that scripted content is not only on ideological topics (although it is increasingly ideological) and is also very prevalent in commercial papers. Using a case study of domestic coverage of COVID-19, we demonstrate how the regime uses scripting to shape, constrain, and delay information during crises. Our findings reveal the wide-ranging influence of government-authored propaganda in China’s media ecosystem.

To ensure optimal replication and spread, viruses have evolved countermeasures to evade type 1 IFN-mediated antiviral activity. During the early viral replication cycle steps until uncoating, the HIV-1 core protects viral pathogen associated molecular patterns (viral RNA and reverse transcription products) from recognition by innate immune sensors, including cGAS. However, after capsid uncoating, unintegrated viral DNA (uvDNA) becomes accessible. Here, we show that HIV-1 uses chromatin-mediated cGAS inactivation as a mechanism to protect its uvDNA from innate immune activation.

Examination of the subjective qualitative aspects of an experience, or “qualia” in short, is a fundamental and core aspect of consciousness research. How can we characterize the particular quality of redness, i.e. a red quale? Based on a recent proposal of the structural characterization of qualia, which did not rely on verbal descriptions, we developed a task that obtained pairwise similarity judgments at four graded levels, with easy and intuitive visual interfaces designed to engage young children. We examined color qualia structures in children (3 to 12-y-old in Japan and 6 to 8-y-old in China) and compared these with those of Japanese adults. Approximately half of the assessed 3-y-old children completed the experiment via our touch panel device version of the task and had reliable responses. Despite known developmental and/or cultural effects of color term usage, we found that color qualia structures were quite similar across the age groups and cultures. Our finding supports the view that color qualia structures emerge early. We also observed age-related differences in the evaluations of some color pairs, which implied subtle changes in the structures behind color experience.

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To navigate real-world listening conditions, the auditory system relies on the integration of multiple sources of information. However, to avoid inappropriate cross-talk between inputs, highly connected neural systems need to strike a balance between integration and segregation. Here, we develop a novel approach to examine how repeated neurochemical modules in the mouse inferior colliculus lateral cortex (LC) allow controlled integration of its multimodal inputs. The LC had been impossible to study via imaging because it is buried in a sulcus. Therefore, we coupled two-photon microscopy with the use of a microprism to reveal the first-ever sagittal views of the LC to examine neuronal responses with respect to its neurochemical motifs under anesthetized and awake conditions. This approach revealed marked differences in the acoustic response properties of LC and neighboring non-lemniscal portions of the inferior colliculus. In addition, we observed that the module and matrix cellular motifs of the LC displayed distinct somatosensory and auditory responses. Specifically, neurons in modules demonstrated primarily offset responses to acoustic stimuli with enhancement in responses to bimodal stimuli, whereas matrix neurons showed onset response to acoustic stimuli and suppressed responses to bimodal stimulation. Thus, this new approach revealed that the repeated structural motifs of the LC permit functional integration of multimodal inputs while retaining distinct response properties.

In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss ofFoxg1in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway componentFgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic cues in newborn neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons non-autonomously enhances gliogenesis in the progenitors via FGF signalling. These results fit well with the model that newborn neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated inFoxg1null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.

To navigate real-world listening conditions, the auditory system relies on the integration of multiple sources of information. However, to avoid inappropriate cross-talk between inputs, highly connected neural systems need to strike a balance between integration and segregation. Here, we develop a novel approach to examine how repeated neurochemical modules in the mouse inferior colliculus lateral cortex (LC) allow controlled integration of its multimodal inputs. The LC had been impossible to study via imaging because it is buried in a sulcus. Therefore, we coupled two-photon microscopy with the use of a microprism to reveal the first-ever sagittal views of the LC to examine neuronal responses with respect to its neurochemical motifs under anesthetized and awake conditions. This approach revealed marked differences in the acoustic response properties of LC and neighboring non-lemniscal portions of the inferior colliculus. In addition, we observed that the module and matrix cellular motifs of the LC displayed distinct somatosensory and auditory responses. Specifically, neurons in modules demonstrated primarily offset responses to acoustic stimuli with enhancement in responses to bimodal stimuli, whereas matrix neurons showed onset response to acoustic stimuli and suppressed responses to bimodal stimulation. Thus, this new approach revealed that the repeated structural motifs of the LC permit functional integration of multimodal inputs while retaining distinct response properties.

Juvenile hormone (JH) is important to maintain insect larval status; however, its cell membrane receptor has not been identified. Using the lepidopteran insectHelicoverpa armigera(cotton bollworm), a serious agricultural pest, as a model, we determined that receptor tyrosine kinases (RTKs) cadherin 96ca (CAD96CA) and fibroblast growth factor receptor homologue (FGFR1) function as JH cell membrane receptors by their roles in JH-regulated gene expression, larval status maintaining, rapid intracellular calcium increase, phosphorylation of JH intracellular receptor MET1 and cofactor Taiman, and high affinity to JH III. Gene knockout ofCad96caandFgfr1by CRISPR/Cas9 in embryo and knockdown in various insect cells, and overexpression of CAD96CA and FGFR1 in mammalian HEK-293T cells all supported CAD96CA and FGFR1 transmitting JH signal as JH cell membrane receptors.

Natural killer (NK) cells recognize target cells through germline-encoded activation and inhibitory receptors enabling effective immunity against viruses and cancer. The Ly49 receptor family in the mouse and killer immunoglobin-like receptor family in humans play a central role in NK cell immunity through recognition of major histocompatibility complex class I (MHC-I) and related molecules. Functionally, these receptor families are involved in the licensing and rejection of MHC-I-deficient cells through missing-self. The Ly49 family is highly polymorphic, making it challenging to detail the contributions of individual Ly49 receptors to NK cell function. Herein, we showed mice lacking expression of all Ly49s were unable to reject missing-self target cells in vivo, were defective in NK cell licensing, and displayed lower KLRG1 on the surface of NK cells. Expression of Ly49A alone on an H-2Ddbackground restored missing-self target cell rejection, NK cell licensing, and NK cell KLRG1 expression. Thus, a single inhibitory Ly49 receptor is sufficient to license NK cells and mediate missing-self in vivo.

Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however, few studies have investigated its role in neurodegenerative processes such as Alzheimer’s disease (AD). Here, we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in humans, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.

Historically, the creation of the parasympathetic division of the autonomic nervous system of the vertebrates is inextricably linked to the unification of the cranial and sacral autonomic outflows. There is an intriguing disproportion between the entrenchment of the notion of a ‘cranio-sacral’ pathway, which informs every textbook schematic of the autonomic nervous system since the early XXthcentury, and the wobbliness of its two roots: an anatomical detail overinterpreted by Walter Holbrook Gaskell (the ‘gap’ between the lumbar and sacral outflows), on which John Newport Langley grafted a piece of physiology (a supposed antagonism of these two outflows on external genitals), repeatedly questioned since, to little avail. I retrace the birth of a flawed scientific concept (the cranio-sacral outflow) and the way in which it ossified instead of dissipated. Then, I suggest that the critique of the ‘cranio-sacral outflow’ invites, in turn, a radical deconstruction of the very notion of a ‘parasympathetic’ outflow, and a more realistic description of the autonomic nervous system.

Juvenile hormone (JH) is important to maintain insect larval status; however, its cell membrane receptor has not been identified. Using the lepidopteran insectHelicoverpa armigera(cotton bollworm), a serious agricultural pest, as a model, we determined that receptor tyrosine kinases (RTKs) cadherin 96ca (CAD96CA) and fibroblast growth factor receptor homologue (FGFR1) function as JH cell membrane receptors by their roles in JH-regulated gene expression, larval status maintaining, rapid intracellular calcium increase, phosphorylation of JH intracellular receptor MET1 and cofactor Taiman, and high affinity to JH III. Gene knockout ofCad96caandFgfr1by CRISPR/Cas9 in embryo and knockdown in various insect cells, and overexpression of CAD96CA and FGFR1 in mammalian HEK-293T cells all supported CAD96CA and FGFR1 transmitting JH signal as JH cell membrane receptors.

In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss ofFoxg1in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway componentFgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic cues in newborn neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons non-autonomously enhances gliogenesis in the progenitors via FGF signalling. These results fit well with the model that newborn neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated inFoxg1null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.

Natural killer (NK) cells recognize target cells through germline-encoded activation and inhibitory receptors enabling effective immunity against viruses and cancer. The Ly49 receptor family in the mouse and killer immunoglobin-like receptor family in humans play a central role in NK cell immunity through recognition of major histocompatibility complex class I (MHC-I) and related molecules. Functionally, these receptor families are involved in the licensing and rejection of MHC-I-deficient cells through missing-self. The Ly49 family is highly polymorphic, making it challenging to detail the contributions of individual Ly49 receptors to NK cell function. Herein, we showed mice lacking expression of all Ly49s were unable to reject missing-self target cells in vivo, were defective in NK cell licensing, and displayed lower KLRG1 on the surface of NK cells. Expression of Ly49A alone on an H-2Ddbackground restored missing-self target cell rejection, NK cell licensing, and NK cell KLRG1 expression. Thus, a single inhibitory Ly49 receptor is sufficient to license NK cells and mediate missing-self in vivo.

Mycobacterium tuberculosis(Mtb) infection of macrophages reprograms cellular metabolism to promote lipid retention. While it is clearly known that intracellularMtbutilize host-derived lipids to maintain infection, the role of macrophage lipid processing on the bacteria’s ability to access the intracellular lipid pool remains undefined. We utilized a CRISPR-Cas9 genetic approach to assess the impact of sequential steps in fatty acid metabolism on the growth of intracellularMtb. Our analyses demonstrate that macrophages that cannot either import, store, or catabolize fatty acids restrictMtbgrowth by both common and divergent antimicrobial mechanisms, including increased glycolysis, increased oxidative stress, production of pro-inflammatory cytokines, enhanced autophagy, and nutrient limitation. We also show that impaired macrophage lipid droplet biogenesis is restrictive toMtbreplication, but increased induction of the same fails to rescueMtbgrowth. Our work expands our understanding of how host fatty acid homeostasis impactsMtbgrowth in the macrophage.

Virion Infectivity Factor (Vif) of the Human Immunodeficiency Virus type 1 (HIV-1) targets and degrades cellular APOBEC3 proteins, key regulators of intrinsic and innate antiretroviral immune responses, thereby facilitating HIV-1 infection. While Vif’s role in degrading APOBEC3G is well-studied, Vif is also known to cause cell cycle arrest, but the detailed nature of Vif’s effects on the cell cycle has yet to be delineated. In this study, we employed high-temporal resolution single-cell live imaging and super-resolution microscopy to monitor individual cells during Vif-induced cell cycle arrest. Our findings reveal that Vif does not affect the G2/M boundary as previously thought. Instead, Vif triggers a unique and robust pseudo-metaphase arrest, distinct from the mild prometaphase arrest induced by Vpr. During this arrest, chromosomes align properly and form the metaphase plate, but later lose alignment, resulting in polar chromosomes. Notably, Vif, unlike Vpr, significantly reduces the levels of both Protein Phosphatase 1 (PP1) and 2 A (PP2A) at kinetochores, which regulate chromosome-microtubule interactions. These results unveil a novel role for Vif in kinetochore regulation that governs the spatial organization of chromosomes during mitosis.

RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized duringCaenorhabditis elegansembryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.

Dietary protein absorption in neonatal mammals and fishes relies on the function of a specialized and conserved population of highly absorptive lysosome-rich enterocytes (LREs). The gut microbiome has been shown to enhance absorption of nutrients, such as lipids, by intestinal epithelial cells. However, whether protein absorption is also affected by the gut microbiome is poorly understood. Here, we investigate connections between protein absorption and microbes in the zebrafish gut. Using live microscopy-based quantitative assays, we find that microbes slow the pace of protein uptake and degradation in LREs. While microbes do not affect the number of absorbing LRE cells, microbes lower the expression of endocytic and protein digestion machinery in LREs. Using transgene-assisted cell isolation and single cell RNA-sequencing, we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria-sensing and metabolic pathways in LREs, and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs. Using custom-formulated diets, we investigated the influence of diet and LRE activity on the gut microbiome. Impaired protein uptake activity in LREs, along with a protein-deficient diet, alters the microbial community and leads to an increased abundance of bacterial genera that have the capacity to reduce protein uptake in LREs. Together, these results reveal that diet-dependent reciprocal interactions between LREs and the gut microbiome regulate protein absorption.

Dietary protein absorption in neonatal mammals and fishes relies on the function of a specialized and conserved population of highly absorptive lysosome-rich enterocytes (LREs). The gut microbiome has been shown to enhance absorption of nutrients, such as lipids, by intestinal epithelial cells. However, whether protein absorption is also affected by the gut microbiome is poorly understood. Here, we investigate connections between protein absorption and microbes in the zebrafish gut. Using live microscopy-based quantitative assays, we find that microbes slow the pace of protein uptake and degradation in LREs. While microbes do not affect the number of absorbing LRE cells, microbes lower the expression of endocytic and protein digestion machinery in LREs. Using transgene-assisted cell isolation and single cell RNA-sequencing, we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria-sensing and metabolic pathways in LREs, and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs. Using custom-formulated diets, we investigated the influence of diet and LRE activity on the gut microbiome. Impaired protein uptake activity in LREs, along with a protein-deficient diet, alters the microbial community and leads to an increased abundance of bacterial genera that have the capacity to reduce protein uptake in LREs. Together, these results reveal that diet-dependent reciprocal interactions between LREs and the gut microbiome regulate protein absorption.

Antimicrobial peptides (AMPs) are attractive candidates to combat antibiotic resistance for their capability to target biomembranes and restrict a wide range of pathogens. It is a daunting challenge to discover novel AMPs due to their sparse distributions in a vast peptide universe, especially for peptides that demonstrate potencies for both bacterial membranes and viral envelopes. Here, we establish a de novo AMP design framework by bridging a deep generative module and a graph-encoding activity regressor. The generative module learns hidden ‘grammars’ of AMP features and produces candidates sequentially pass antimicrobial predictor and antiviral classifiers. We discovered 16 bifunctional AMPs and experimentally validated their abilities to inhibit a spectrum of pathogens in vitro and in animal models. Notably, P076 is a highly potent bactericide with the minimal inhibitory concentration of 0.21 μM against multidrug-resistantAcinetobacter baumannii, while P002 broadly inhibits five enveloped viruses. Our study provides feasible means to uncover the sequences that simultaneously encode antimicrobial and antiviral activities, thus bolstering the function spectra of AMPs to combat a wide range of drug-resistant infections.

Investigating how the production of insulin is regulated in fruit flies reveals surprising insights that may help to better understand how this process unfolds in humans.

Antimicrobial peptides (AMPs) are attractive candidates to combat antibiotic resistance for their capability to target biomembranes and restrict a wide range of pathogens. It is a daunting challenge to discover novel AMPs due to their sparse distributions in a vast peptide universe, especially for peptides that demonstrate potencies for both bacterial membranes and viral envelopes. Here, we establish a de novo AMP design framework by bridging a deep generative module and a graph-encoding activity regressor. The generative module learns hidden ‘grammars’ of AMP features and produces candidates sequentially pass antimicrobial predictor and antiviral classifiers. We discovered 16 bifunctional AMPs and experimentally validated their abilities to inhibit a spectrum of pathogens in vitro and in animal models. Notably, P076 is a highly potent bactericide with the minimal inhibitory concentration of 0.21 μM against multidrug-resistantAcinetobacter baumannii, while P002 broadly inhibits five enveloped viruses. Our study provides feasible means to uncover the sequences that simultaneously encode antimicrobial and antiviral activities, thus bolstering the function spectra of AMPs to combat a wide range of drug-resistant infections.

RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized duringCaenorhabditis elegansembryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.

Haploinsufficiency forGATA6is associated with congenital heart disease (CHD) with variable comorbidity of pancreatic or diaphragm defects, although the etiology of disease is not well understood. Here, we used cardiac directed differentiation from human embryonic stem cells (hESCs) as a platform to study GATA6 function during early cardiogenesis. GATA6 loss-of-function hESCs had a profound impairment in cardiac progenitor cell (CPC) specification and cardiomyocyte (CM) generation due to early defects during the mesendoderm and lateral mesoderm patterning stages. Profiling by RNA-seq and CUT&RUN identified genes of the WNT and BMP programs regulated by GATA6 during early mesoderm patterning. Furthermore, interactome analysis detected GATA6 binding with developmental transcription factors and chromatin remodelers, suggesting cooperative regulation of cardiac lineage gene accessibility. We show that modulating WNT and BMP inputs during the first 48 hr of cardiac differentiation is sufficient to partially rescue CPC and CM defects inGATA6heterozygous and homozygous mutant hESCs. This study provides evidence of the regulatory functions for GATA6 directing human precardiac mesoderm patterning during the earliest stages of cardiogenesis to further our understanding of haploinsufficiency causing CHD and the co-occurrence of cardiac and other organ defects caused by humanGATA6mutations.

Virion Infectivity Factor (Vif) of the Human Immunodeficiency Virus type 1 (HIV-1) targets and degrades cellular APOBEC3 proteins, key regulators of intrinsic and innate antiretroviral immune responses, thereby facilitating HIV-1 infection. While Vif’s role in degrading APOBEC3G is well-studied, Vif is also known to cause cell cycle arrest, but the detailed nature of Vif’s effects on the cell cycle has yet to be delineated. In this study, we employed high-temporal resolution single-cell live imaging and super-resolution microscopy to monitor individual cells during Vif-induced cell cycle arrest. Our findings reveal that Vif does not affect the G2/M boundary as previously thought. Instead, Vif triggers a unique and robust pseudo-metaphase arrest, distinct from the mild prometaphase arrest induced by Vpr. During this arrest, chromosomes align properly and form the metaphase plate, but later lose alignment, resulting in polar chromosomes. Notably, Vif, unlike Vpr, significantly reduces the levels of both Protein Phosphatase 1 (PP1) and 2 A (PP2A) at kinetochores, which regulate chromosome-microtubule interactions. These results unveil a novel role for Vif in kinetochore regulation that governs the spatial organization of chromosomes during mitosis.

Haploinsufficiency forGATA6is associated with congenital heart disease (CHD) with variable comorbidity of pancreatic or diaphragm defects, although the etiology of disease is not well understood. Here, we used cardiac directed differentiation from human embryonic stem cells (hESCs) as a platform to study GATA6 function during early cardiogenesis. GATA6 loss-of-function hESCs had a profound impairment in cardiac progenitor cell (CPC) specification and cardiomyocyte (CM) generation due to early defects during the mesendoderm and lateral mesoderm patterning stages. Profiling by RNA-seq and CUT&RUN identified genes of the WNT and BMP programs regulated by GATA6 during early mesoderm patterning. Furthermore, interactome analysis detected GATA6 binding with developmental transcription factors and chromatin remodelers, suggesting cooperative regulation of cardiac lineage gene accessibility. We show that modulating WNT and BMP inputs during the first 48 hr of cardiac differentiation is sufficient to partially rescue CPC and CM defects inGATA6heterozygous and homozygous mutant hESCs. This study provides evidence of the regulatory functions for GATA6 directing human precardiac mesoderm patterning during the earliest stages of cardiogenesis to further our understanding of haploinsufficiency causing CHD and the co-occurrence of cardiac and other organ defects caused by humanGATA6mutations.

Fiber photometry has become a popular technique to measure neural activity in vivo, but common analysis strategies can reduce the detection of effects because they condensewithin-trialsignals into summary measures, and discard trial-level information by averagingacross-trials. We propose a novel photometry statistical framework based on functional linear mixed modeling, which enables hypothesis testing of variable effects atevery trial time-point, and uses trial-level signals without averaging. This makes it possible to compare the timing and magnitude of signals across conditions while accounting for between-animal differences. Our framework produces a series of plots that illustrate covariate effect estimates and statistical significance at each trial time-point. By exploiting signal autocorrelation, our methodology yieldsjoint95% confidence intervals that account for inspecting effects across the entire trial and improve the detection of event-related signal changes over common multiple comparisons correction strategies. We reanalyze data from a recent study proposing a theory for the role of mesolimbic dopamine in reward learning, and show the capability of our framework to reveal significant effects obscured by standard analysis approaches. For example, our method identifies two dopamine components with distinct temporal dynamics in response to reward delivery. In simulation experiments, our methodology yields improved statistical power over common analysis approaches. Finally, we provide an open-source package and analysis guide for applying our framework.

Longitudinal neuroimaging studies offer valuable insight into brain development, ageing, and disease progression over time. However, prevailing analytical approaches rooted in our understanding of population variation are primarily tailored for cross-sectional studies. To fully leverage the potential of longitudinal neuroimaging, we need methodologies that account for the complex interplay between population variation and individual dynamics. We extend the normative modelling framework, which evaluates an individual’s position relative to population standards, to assess an individual’s longitudinalchangecompared to the population’s standard dynamics. Using normative models pre-trained on over 58,000 individuals, we introduce a quantitative metric termed ‘z-diff’ score, which quantifies a temporal change in individuals compared to a population standard. This approach offers advantages in flexibility in dataset size and ease of implementation. We applied this framework to a longitudinal dataset of 98 patients with early-stage schizophrenia who underwent MRI examinations shortly after diagnosis and 1 year later. Compared to cross-sectional analyses, showing global thinning of grey matter at the first visit, our method revealed a significant normalisation of grey matter thickness in the frontal lobe over time—an effect undetected by traditional longitudinal methods. Overall, our framework presents a flexible and effective methodology for analysing longitudinal neuroimaging data, providing insights into the progression of a disease that would otherwise be missed when using more traditional approaches.

Human autonomic neuronal cell models are emerging as tools for modelling diseases such as cardiac arrhythmias. In this systematic review, we compared thirty-three articles applying fourteen different protocols to generate sympathetic neurons and three different procedures to produce parasympathetic neurons. All methods involved the differentiation of human pluripotent stem cells, and none employed permanent or reversible cell immortalization. Almost all protocols were reproduced in multiple pluripotent stem cell lines, and over half show evidence of neural firing capacity. Common limitations in the field are a lack of three-dimensional models and models including multiple cell types. Sympathetic neuron differentiation protocols largely mirrored embryonic development, with the notable absence of migration, axon extension, and target-specificity cues. Parasympathetic neuron differentiation protocols may be improved by including several embryonic cues promoting cell survival, cell maturation, or ion channel expression. Moreover, additional markers to define parasympathetic neuronsin vitromay support the validity of these protocols. Nonetheless, four sympathetic neuron differentiation protocols and one parasympathetic neuron differentiation protocol reported more than two thirds of cells expressing autonomic neuron markers. Altogether, these protocols promise to open new research avenues of human autonomic neuron development and disease modelling.

Research on brain plasticity, particularly in the context of deafness, consistently emphasizes the reorganization of the auditory cortex. But to what extent do all individuals with deafness show the same level of reorganization? To address this question, we examined the individual differences in functional connectivity (FC) from the deprived auditory cortex. Our findings demonstrate remarkable differentiation between individuals deriving from the absence of shared auditory experiences, resulting in heightened FC variability among deaf individuals, compared to more consistent FC in the hearing group. Notably, connectivity to language regions becomes more diverse across individuals with deafness. This does not stem from delayed language acquisition; it is found in deaf native signers, who are exposed to natural language since birth. However, comparing FC diversity between deaf native signers and deaf delayed signers, who were deprived of language in early development, we show that language experience also impacts individual differences, although to a more moderate extent. Overall, our research points out the intricate interplay between brain plasticity and individual differences, shedding light on the diverse ways reorganization manifests among individuals. It joins findings of increased connectivity diversity in blindness and highlights the importance of considering individual differences in personalized rehabilitation for sensory loss.

Evolution of gene expression frequently drives antibiotic resistance in bacteria. We had previously (Patel and Matange,eLife, 2021) shown that, inEscherichia coli, mutations at themgrBlocus were beneficial under trimethoprim exposure and led to overexpression of dihydrofolate reductase (DHFR), encoded by thefolAgene. Here, we show that DHFR levels are further enhanced by spontaneous duplication of a genomic segment encompassingfolAand spanning hundreds of kilobases. This duplication was rare in wild-typeE. coli. However, its frequency was elevated in alon-knockout strain, altering the mutational landscape early during trimethoprim adaptation. We then exploit this system to investigate the relationship between trimethoprim pressure andfolAcopy number. During long-term evolution,folAduplications were frequently reversed. Reversal was slower under antibiotic pressure, first requiring the acquisition of point mutations in DHFR or its promoter. Unexpectedly, despite resistance-conferring point mutations, some populations under high trimethoprim pressure maintainedfolAduplication to compensate for low abundance DHFR mutants. We find that evolution of gene dosage depends on expression demand, which is generated by antibiotic and exacerbated by proteolysis of drug-resistant mutants of DHFR. We propose a novel role for proteostasis as a determinant of copy number evolution in antibiotic-resistant bacteria.

Evolution of gene expression frequently drives antibiotic resistance in bacteria. We had previously (Patel and Matange,eLife, 2021) shown that, inEscherichia coli, mutations at themgrBlocus were beneficial under trimethoprim exposure and led to overexpression of dihydrofolate reductase (DHFR), encoded by thefolAgene. Here, we show that DHFR levels are further enhanced by spontaneous duplication of a genomic segment encompassingfolAand spanning hundreds of kilobases. This duplication was rare in wild-typeE. coli. However, its frequency was elevated in alon-knockout strain, altering the mutational landscape early during trimethoprim adaptation. We then exploit this system to investigate the relationship between trimethoprim pressure andfolAcopy number. During long-term evolution,folAduplications were frequently reversed. Reversal was slower under antibiotic pressure, first requiring the acquisition of point mutations in DHFR or its promoter. Unexpectedly, despite resistance-conferring point mutations, some populations under high trimethoprim pressure maintainedfolAduplication to compensate for low abundance DHFR mutants. We find that evolution of gene dosage depends on expression demand, which is generated by antibiotic and exacerbated by proteolysis of drug-resistant mutants of DHFR. We propose a novel role for proteostasis as a determinant of copy number evolution in antibiotic-resistant bacteria.

Fiber photometry has become a popular technique to measure neural activity in vivo, but common analysis strategies can reduce the detection of effects because they condensewithin-trialsignals into summary measures, and discard trial-level information by averagingacross-trials. We propose a novel photometry statistical framework based on functional linear mixed modeling, which enables hypothesis testing of variable effects atevery trial time-point, and uses trial-level signals without averaging. This makes it possible to compare the timing and magnitude of signals across conditions while accounting for between-animal differences. Our framework produces a series of plots that illustrate covariate effect estimates and statistical significance at each trial time-point. By exploiting signal autocorrelation, our methodology yieldsjoint95% confidence intervals that account for inspecting effects across the entire trial and improve the detection of event-related signal changes over common multiple comparisons correction strategies. We reanalyze data from a recent study proposing a theory for the role of mesolimbic dopamine in reward learning, and show the capability of our framework to reveal significant effects obscured by standard analysis approaches. For example, our method identifies two dopamine components with distinct temporal dynamics in response to reward delivery. In simulation experiments, our methodology yields improved statistical power over common analysis approaches. Finally, we provide an open-source package and analysis guide for applying our framework.

Longitudinal neuroimaging studies offer valuable insight into brain development, ageing, and disease progression over time. However, prevailing analytical approaches rooted in our understanding of population variation are primarily tailored for cross-sectional studies. To fully leverage the potential of longitudinal neuroimaging, we need methodologies that account for the complex interplay between population variation and individual dynamics. We extend the normative modelling framework, which evaluates an individual’s position relative to population standards, to assess an individual’s longitudinalchangecompared to the population’s standard dynamics. Using normative models pre-trained on over 58,000 individuals, we introduce a quantitative metric termed ‘z-diff’ score, which quantifies a temporal change in individuals compared to a population standard. This approach offers advantages in flexibility in dataset size and ease of implementation. We applied this framework to a longitudinal dataset of 98 patients with early-stage schizophrenia who underwent MRI examinations shortly after diagnosis and 1 year later. Compared to cross-sectional analyses, showing global thinning of grey matter at the first visit, our method revealed a significant normalisation of grey matter thickness in the frontal lobe over time—an effect undetected by traditional longitudinal methods. Overall, our framework presents a flexible and effective methodology for analysing longitudinal neuroimaging data, providing insights into the progression of a disease that would otherwise be missed when using more traditional approaches.

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AbstractNeuropathic pain, which has become a major public health concern, is frequently accompanied by the deterioration of affective behavior and cognitive function. However, the brain circuitry underlying these changes is poorly understood. Therefore, we aimed to identify in a mouse model the converging circuit that influences the sensory, affective, and cognitive consequences of neuropathic pain. The lateral habenula (LHb) and ventral tegmental area (VTA) have been confirmed to play critical roles in the regulation of pain, cognition, and depression. Given the essential role of the LHb in depression and cognition, we attempted to clarify how neural circuitry involving the LHb integrates pain-related information. Our data confirmed that the VTA receives projections from the LHb, but our results suggest that inhibition of this direct pathway has no effect on the behavior of mice with chronic neuropathic pain. The rostromedial tegmental nucleus (RMTg), a GABAergic structure believed to underlie the transient inhibition of DAergic neurons in the VTA, received glutamatergic inputs from the LHb and projected strongly to the VTA. Furthermore, our data suggest that a projection from LHb glutamatergic neurons to RMTg GABAergic neurons in the VTA, constituting an indirect LHbGlu→ RMTgGABA→ VTADApathway, participates in peripheral nerve injury-induced nociceptive hypersensitivity, depressive-like behavior, and cognitive dysfunction. Ex vivo extracellular recordings of LHb neurons showed that the proportion of burst-firing cells in the LHb was significantly increased in indirect projections rather than in direct projections. This may explain the functional discrepancies between direct and indirect projections of the LHb to the VTA. Collectively, our study identifies a pivotal role of the LHbGlu→ RMTgGABA→ VTADApathway in processing pain. This pathway may offer new therapeutic targets to treat neuropathic pain and its associated depressive-like and cognitive impairments.

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AbstractAcute intoxication from Δ9-tetrahydrocannabinol (THC, the primary active ingredient of cannabis) can lead to neurocognitive impairment and interference with day-to-day operations, such as driving. Present evaluations of THC-induced impairment in legal settings rely on biological drug tests that solely establish cannabis use, rather than cannabis impairment. The current study evaluated the metabolome in blood collected from occasional and chronic cannabis users (N= 35) at baseline and following treatments with cannabis (300 μg/kg THC) and placebo, with the aim to identify unique metabolic alterations that are associated with acute cannabis intoxication and cannabis use frequency. Blood samples were collected at baseline and repeatedly during 70 min after treatment. Sustained attention performance and ratings of subjective high were taken twice within 40 min after treatment. Metabolomic fingerprints of occasional and chronic cannabis users were distinctly different at baseline, when both groups were not intoxicated. A total of 14 metabolites, mainly related to endocannabinoid and amino acid metabolism, were identified that distinguished chronic from occasional cannabis users and that yielded a discriminant analysis model with an 80% classification rate (95% CI: 61–91%). Distinct metabolomic fingerprints were found for occasional cannabis users who, in contrast to chronic cannabis users, showed attentional impairment and elevated ratings of subjective high during cannabis intoxication. These included increments in organic acids, β-hydroxybutyrate and second messenger ceramides. The current study demonstrates the feasibility of the metabolomics approach to identify metabolic changes that are specific to the neurocognitive state of cannabis intoxication and to the history of cannabis use.